The state Labour parties and their MPs were mixed in their support for the Federation of Australia.
However Fisher was a firm federationist, supporting the union of the Australian colonies and campaigned for the 'Yes' vote in Queensland's 1899 referendum.
 Fisher stood for the electorate of Wide Bay at the inaugural 1901 federal election and won the seat, which he held continuously for the rest of his political career.
At the end of 1901, Fisher married Margaret Irvine, his previous landlady's daughter.

Fisher supported the White Australia policy but also argued that any Kanaka who had converted to Christianity and married should be allowed to remain in Australia.

Labour improved their position at the 1903 election, gaining enough seats to be on par with the other two, a legislative time colloquially known as the "three elevens".
When the Deakin government resigned in 1904, George Reid of the Free Trade Party declined to take office, resulting in Labour taking power and Chris Watson becoming Labour's first Prime Minister for a four-month period in 1904.
Fisher established and demonstrated his ministerial capabilities as Minister for Trade and Customs in the Watson Ministry.
The fourth Labour member in the ministry after Watson, Hughes, and Lee Batchelor, Fisher was promoted to Deputy Leader of the Labour Party in 1905.

George Reid adopted a strategy of trying to reorient the party system along Labour vs non-Labour lines – prior to the 1906 election, he renamed his Free Trade Party to the Anti-Socialist Party.
Reid envisaged a spectrum running from socialist to anti-socialist, with the Protectionist Party in the middle.
This attempt struck a chord with politicians who were steeped in the Westminster tradition and regarded a two-party system as very much the norm.
The state Labour parties and their MPs were mixed in their support for the Federation of Australia. However Fisher was a firm federationist, supporting the union of the Australian colonies and campaigned for the 'Yes' vote in Queensland's 1899 referendum.  Fisher stood for the electorate of Wide Bay at the inaugural 1901 federal election and won the seat, which he held continuously for the rest of his political career. At the end of 1901, Fisher married Margaret Irvine, his previous landlady's daughter.
Fisher supported the White Australia policy but also argued that any Kanaka who had converted to Christianity and married should be allowed to remain in Australia.
Labour improved their position at the 1903 election, gaining enough seats to be on par with the other two, a legislative time colloquially known as the "three elevens". When the Deakin government resigned in 1904, George Reid of the Free Trade Party declined to take office, resulting in Labour taking power and Chris Watson becoming Labour's first Prime Minister for a four-month period in 1904. Fisher established and demonstrated his ministerial capabilities as Minister for Trade and Customs in the Watson Ministry. The fourth Labour member in the ministry after Watson, Hughes, and Lee Batchelor, Fisher was promoted to Deputy Leader of the Labour Party in 1905.
George Reid adopted a strategy of trying to reorient the party system along Labour vs non-Labour lines – prior to the 1906 election, he renamed his Free Trade Party to the Anti-Socialist Party. Reid envisaged a spectrum running from socialist to anti-socialist, with the Protectionist Party in the middle. This attempt struck a chord with politicians who were steeped in the Westminster tradition and regarded a two-party system as very much the norm.
Andrew Fisher