The rails and signalling have been upgraded over the years, and many sections of the line have been deviated: The original 1870s Vogel Era track had rails of 40 lb/yd (19.9 kg/m), some were iron not steel; later rails were 53 lb/yd (26.3 kg/m); and from 1901 70 lb/yd (34.8 kg/m), e.g. between Taumarunui and Taihape for the heavy X-class locos used on the central mountainous section from 1908.
Some 10 bridges between Frankton and Taumarunui had to be strengthened, and in 1914 there was still 129 km (80 mi) of 53 lb/yd rail to be replaced.
In the 1930s 85 lb/yd (42.2 kg/m) was adopted, then 91 lb/yd (45.1 kg/m), and from 1974 100 lb/yd (50 kg/m).
    
Signalling on the single-track sections (most of the line) was controlled by Tyer's Electric Train Tablet No 7 system; with each of the stations for the 94 tablet sections staffed by three tablet porters each working a 56-hour week for continuous coverage; hence each station required at least four houses for the stationmaster and three porters.
Pierre noticed that with CTC station buildings and even platforms had been removed as there were no longer any staffed stations between Ohakune and National Park.
The Train Control system introduced from 1928 to 1932 supplemented the tablet system by operators at the four sections (Auckland, Frankton, Te Kuiti, Ohakune, Marton and Wellington) to expedite operation of trains over several tablet sections; the 1925 Fay-Raven report urged its adoption because of the fitful progress of mixed trains, with locomotives often kept waiting.
From 1938 to 1966 Centralised Traffic Control (C.T.C) gradually replaced the Tablet system on the NIMT.
In 1957 when the installation of CTC over the remaining 354 km commenced, it was estimated that using CTC over the 330 km Taumarunui to Otaki section with control centres at Ohakune (shifted to Taumarunui in 1977), Taihape and Palmerston North would replace 74 men in traffic working duties.
The last section converted was Piriaka-Owhango.

In 1913, the maximum speed limit on the NIMT was raised to 45 mph (72 km/h), reducing the journey time by 1 hour 25 minutes Auckland-Wellington or to 17 hours and between 30 and 45 minutes.
Under T. Ronayne, the Railways Department general manager from 1895 to 1913, the section south to Parnell was duplicated and improvements made to the worst gradients and tight curves between Auckland and Mercer.
Under his successor E. H. Hiley the second Parnell Tunnel with two tracks and an easier gradient was completed in 1915–1916.
On the Kakariki bank between Halcombe and Marton a deviation reduced the 1 in 53 grade to 1 in 70.
A 1914 Act authorised spending on the Westfield Deviation, new stations at Auckland and Wellington, track doubling (Penrose-Papakura, Ohinewai-Huntly, Horotiu-Frankton, Newmarket-New Lynn), and grade easements from Penrose to Te Kuiti, but the war delayed most of these works for over a decade.

In 1927, automatic colour-light signalling was installed from Otahuhu to Mercer.
In 1930 the signalling was extended 34 mi 72 ch (56.2 km) to Frankton and the 6 mi 55 ch (10.8 km) from there to Horotiu was doubled.
The 3 mi 54 ch (5.9 km) north to Ngāruawāhia was doubled from 5 December 1937, followed by 9 mi 12 ch (14.7 km) Ngāruawāhia to Huntly on 4 December 1938 and Huntly to Ohinewai and Papakura to Paerata in December 1939.
By then, wartime shortages delayed further double-tracking.
Pokeno to Mercer was doubled from 11 November 1951, Pukekohe to Pokeno 21 November 1954, Mercer to Amokura 1 July 1956 and Ohinewai to Te Kauwhata 14 December 1958.
The 13 km (8.1 mi) between Amokura and Te Kauwhata remain single track, as does Ngāruawāhia bridge.

In 1930, the Westfield Deviation was opened, creating a new eastern route from Auckland to Westfield via Glen Innes and Hobsons Bay, running into the new Auckland railway station and providing better access to the Port of Auckland.
The original section between Auckland and Westfield via Newmarket later ceased to be part of the NIMT: Auckland to Newmarket became the Auckland-Newmarket Line, and Newmarket to Westfield became par
The rails and signalling have been upgraded over the years, and many sections of the line have been deviated: The original 1870s Vogel Era track had rails of 40 lb/yd (19.9 kg/m), some were iron not steel; later rails were 53 lb/yd (26.3 kg/m); and from 1901 70 lb/yd (34.8 kg/m), e.g. between Taumarunui and Taihape for the heavy X-class locos used on the central mountainous section from 1908. Some 10 bridges between Frankton and Taumarunui had to be strengthened, and in 1914 there was still 129 km (80 mi) of 53 lb/yd rail to be replaced. In the 1930s 85 lb/yd (42.2 kg/m) was adopted, then 91 lb/yd (45.1 kg/m), and from 1974 100 lb/yd (50 kg/m).     
Signalling on the single-track sections (most of the line) was controlled by Tyer's Electric Train Tablet No 7 system; with each of the stations for the 94 tablet sections staffed by three tablet porters each working a 56-hour week for continuous coverage; hence each station required at least four houses for the stationmaster and three porters. Pierre noticed that with CTC station buildings and even platforms had been removed as there were no longer any staffed stations between Ohakune and National Park. The Train Control system introduced from 1928 to 1932 supplemented the tablet system by operators at the four sections (Auckland, Frankton, Te Kuiti, Ohakune, Marton and Wellington) to expedite operation of trains over several tablet sections; the 1925 Fay-Raven report urged its adoption because of the fitful progress of mixed trains, with locomotives often kept waiting. From 1938 to 1966 Centralised Traffic Control (C.T.C) gradually replaced the Tablet system on the NIMT. In 1957 when the installation of CTC over the remaining 354 km commenced, it was estimated that using CTC over the 330 km Taumarunui to Otaki section with control centres at Ohakune (shifted to Taumarunui in 1977), Taihape and Palmerston North would replace 74 men in traffic working duties. The last section converted was Piriaka-Owhango. 
In 1913, the maximum speed limit on the NIMT was raised to 45 mph (72 km/h), reducing the journey time by 1 hour 25 minutes Auckland-Wellington or to 17 hours and between 30 and 45 minutes. Under T. Ronayne, the Railways Department general manager from 1895 to 1913, the section south to Parnell was duplicated and improvements made to the worst gradients and tight curves between Auckland and Mercer. Under his successor E. H. Hiley the second Parnell Tunnel with two tracks and an easier gradient was completed in 1915–1916. On the Kakariki bank between Halcombe and Marton a deviation reduced the 1 in 53 grade to 1 in 70. A 1914 Act authorised spending on the Westfield Deviation, new stations at Auckland and Wellington, track doubling (Penrose-Papakura, Ohinewai-Huntly, Horotiu-Frankton, Newmarket-New Lynn), and grade easements from Penrose to Te Kuiti, but the war delayed most of these works for over a decade.
In 1927, automatic colour-light signalling was installed from Otahuhu to Mercer. In 1930 the signalling was extended 34 mi 72 ch (56.2 km) to Frankton and the 6 mi 55 ch (10.8 km) from there to Horotiu was doubled. The 3 mi 54 ch (5.9 km) north to Ngāruawāhia was doubled from 5 December 1937, followed by 9 mi 12 ch (14.7 km) Ngāruawāhia to Huntly on 4 December 1938 and Huntly to Ohinewai and Papakura to Paerata in December 1939. By then, wartime shortages delayed further double-tracking. Pokeno to Mercer was doubled from 11 November 1951, Pukekohe to Pokeno 21 November 1954, Mercer to Amokura 1 July 1956 and Ohinewai to Te Kauwhata 14 December 1958. The 13 km (8.1 mi) between Amokura and Te Kauwhata remain single track, as does Ngāruawāhia bridge.
In 1930, the Westfield Deviation was opened, creating a new eastern route from Auckland to Westfield via Glen Innes and Hobsons Bay, running into the new Auckland railway station and providing better access to the Port of Auckland. The original section between Auckland and Westfield via Newmarket later ceased to be part of the NIMT: Auckland to Newmarket became the Auckland-Newmarket Line, and Newmarket to Westfield became par
North Island Main Trunk