In November 1943, Kinkaid replaced Carpender as Commander Allied Naval Forces, Southwest Pacific Area, and the Seventh Fleet, known as "MacArthur's Navy".
General Douglas MacArthur had twice requested Carpender's relief, and Kinkaid's record working with the Army in Alaska made him a logical choice.
Australian newspapers hailed the appointment of a "fighting admiral", but neither MacArthur nor the Australian government had been consulted about the appointment, which was made by the Commander in Chief, United States Fleet, Admiral Ernest King.
This was a violation of the international agreement that had established the Southwest Pacific Area.
The Navy Department then announced that the replacement of Carpender with Kinkaid was merely a proposal, and MacArthur and the Prime Minister of Australia, John Curtin, were asked if Kinkaid was acceptable.
They agreed that he was.
In his new role, Kinkaid had two masters.
As commander of the Seventh Fleet, he was answerable to King, but as Commander Allied Naval Forces, Kinkaid was answerable to MacArthur.
Operations were conducted on the basis of "mutual cooperation" rather than "unity of command", and relations between the Army and Navy were not good.
Kinkaid was not the most senior naval officer in the theater, for the Royal Australian Navy's Admiral Sir Guy Royle and the Royal Netherlands Navy's Admiral Conrad Helfrich were both senior to him.

Despite the unpromising relationship with the army, Kinkaid's most troublesome subordinate was a U.S. Navy officer, as had been the case with Rockwell in the Aleutians.
This time, the subordinate was Rear Admiral Ralph W. Christie, the commander of Task Force 71, the Seventh Fleet's submarines.
Christie commonly greeted a returning submarine at the pier and awarded decorations on the spot.
This practice bypassed military and naval award boards, and annoyed Kinkaid because confirmation of sinkings was accomplished by Ultra, and news of awards given so quickly could constitute a security breach.
Kinkaid gave Christie and his other subordinates orders forbidding pierside awards, and the award of army medals to navy personnel.
In June 1944, Christie accompanied a war patrol on Commander Samuel D. Dealey's submarine USS Harder.
Afterward, Christie met with MacArthur and related the events of the war patrol to the general, who decided to award Dealey the Distinguished Service Cross and Christie the Silver Star.
When Harder was lost with Dealey and all hands on its next patrol, Christie recommended Dealey for the Medal of Honor.
Kinkaid turned down the recommendation on the grounds that Dealey had already received the Distinguished Service Cross for the same patrol.
Angered, Christie sent a dispatch to Kinkaid in an easily decipherable low-order code that criticized him and urged him to reconsider.
Upset by both Christie's attitude and his losses, which included Dealey and Kinkaid's nephew, Lieutenant Commander Manning Kimmel on USS Robalo in July 1944, Kinkaid requested Christie's relief.
On 30 December 1944, Christie was replaced by Captain James Fife Jr.
Other forces under Kinkaid's command included the cruisers of Task Force 74 under Rear Admiral Victor Crutchley, Task Force 75 under Russell S. Berkey, and Task Force 76, the VII Amphibious Force, under Rear Admiral Daniel E. Barbey.
The main role of the Seventh Fleet was supporting MacArthur's drive along the northern coast of New Guinea with a series of 38 amphibious operations, usually directed by Barbey.
Kinkaid accompanied MacArthur for the landing in the Admiralty Islands, where the two men came ashore a few hours after the assault troops.
With 215 vessels involved, Operations Reckless and Persecution in April 1944 together constituted the largest operation in New Guinea waters.
It was followed in quick succession by four more operations, at Wakde, Biak, Noemfor and Sansapor.

For MacArthur's long-awaited return to the Philippines in October 1944, the Seventh Fleet was massively reinforced by Nimitz's Pacific Fleet.
Kinkaid commanded the assault personally, with Barbey's VII Amphibious Fo
In November 1943, Kinkaid replaced Carpender as Commander Allied Naval Forces, Southwest Pacific Area, and the Seventh Fleet, known as "MacArthur's Navy". General Douglas MacArthur had twice requested Carpender's relief, and Kinkaid's record working with the Army in Alaska made him a logical choice. Australian newspapers hailed the appointment of a "fighting admiral", but neither MacArthur nor the Australian government had been consulted about the appointment, which was made by the Commander in Chief, United States Fleet, Admiral Ernest King. This was a violation of the international agreement that had established the Southwest Pacific Area. The Navy Department then announced that the replacement of Carpender with Kinkaid was merely a proposal, and MacArthur and the Prime Minister of Australia, John Curtin, were asked if Kinkaid was acceptable. They agreed that he was. In his new role, Kinkaid had two masters. As commander of the Seventh Fleet, he was answerable to King, but as Commander Allied Naval Forces, Kinkaid was answerable to MacArthur. Operations were conducted on the basis of "mutual cooperation" rather than "unity of command", and relations between the Army and Navy were not good. Kinkaid was not the most senior naval officer in the theater, for the Royal Australian Navy's Admiral Sir Guy Royle and the Royal Netherlands Navy's Admiral Conrad Helfrich were both senior to him.
Despite the unpromising relationship with the army, Kinkaid's most troublesome subordinate was a U.S. Navy officer, as had been the case with Rockwell in the Aleutians. This time, the subordinate was Rear Admiral Ralph W. Christie, the commander of Task Force 71, the Seventh Fleet's submarines. Christie commonly greeted a returning submarine at the pier and awarded decorations on the spot. This practice bypassed military and naval award boards, and annoyed Kinkaid because confirmation of sinkings was accomplished by Ultra, and news of awards given so quickly could constitute a security breach. Kinkaid gave Christie and his other subordinates orders forbidding pierside awards, and the award of army medals to navy personnel. In June 1944, Christie accompanied a war patrol on Commander Samuel D. Dealey's submarine USS Harder. Afterward, Christie met with MacArthur and related the events of the war patrol to the general, who decided to award Dealey the Distinguished Service Cross and Christie the Silver Star. When Harder was lost with Dealey and all hands on its next patrol, Christie recommended Dealey for the Medal of Honor. Kinkaid turned down the recommendation on the grounds that Dealey had already received the Distinguished Service Cross for the same patrol. Angered, Christie sent a dispatch to Kinkaid in an easily decipherable low-order code that criticized him and urged him to reconsider. Upset by both Christie's attitude and his losses, which included Dealey and Kinkaid's nephew, Lieutenant Commander Manning Kimmel on USS Robalo in July 1944, Kinkaid requested Christie's relief. On 30 December 1944, Christie was replaced by Captain James Fife Jr.
Other forces under Kinkaid's command included the cruisers of Task Force 74 under Rear Admiral Victor Crutchley, Task Force 75 under Russell S. Berkey, and Task Force 76, the VII Amphibious Force, under Rear Admiral Daniel E. Barbey. The main role of the Seventh Fleet was supporting MacArthur's drive along the northern coast of New Guinea with a series of 38 amphibious operations, usually directed by Barbey. Kinkaid accompanied MacArthur for the landing in the Admiralty Islands, where the two men came ashore a few hours after the assault troops. With 215 vessels involved, Operations Reckless and Persecution in April 1944 together constituted the largest operation in New Guinea waters. It was followed in quick succession by four more operations, at Wakde, Biak, Noemfor and Sansapor.
For MacArthur's long-awaited return to the Philippines in October 1944, the Seventh Fleet was massively reinforced by Nimitz's Pacific Fleet. Kinkaid commanded the assault personally, with Barbey's VII Amphibious Fo
Thomas C. Kinkaid