Before becoming Lord Mayor in 2017 he was a Labor Party member of the Northern Territory Legislative Assembly from September 2001 to October 2014, representing the Darwin-based electorate of Casuarina.

Once they had arrived in Perth, Vatskalis found that his Greek qualifications were not recognised, and was forced to start again, beginning a degree in environmental health at Curtin University, where he also joined the Labor Party.

[citation needed] In February 2002, the Northern Territory News suggested that Vatskalis had "consistently been one of the Government's better performers", though they also criticised him for not appointing "new blood" to his departments.

[citation needed] The usually conservative tabloid made similar comments in their report on the performance of the Martin ministry on the first anniversary of the election in August, suggesting that he had "impressed observers with his willingness to confront his new responsibilities.

He was criticised for the sacking without explanation of one of the Territory's most senior public servants, the head of the Parks and Wildlife Service, Dr Bill Freeland, and had recurring problems surrounding the planned gas plant at Wickham Point on Darwin Harbour.

As the contracts had already been signed by the Burke Country Liberal Party government, Vatskalis had little choice but to continue supporting the construction of the gas plant, despite significant pressure from angry community groups.

In October 2002, Vatskalis had to be placed under police protection when he received death threats from residents angry over a decision to approve the construction of a private school in a suburban street.

He also became embroiled in a nasty stoush with the taxi industry over planned reforms, clashed with environmentalists over land-clearing around the Daly River area, and was the subject of a damaging A Current Affair report over his handling of the impact on pastoralists from the Alice Springs–Darwin Railway.

[citation needed] In the December 2003 ministerial reshuffle sparked by the axing of Health Minister Jane Aagaard, Vatskalis was severely demoted, losing all his portfolios except Ethnic Affairs, and being given the new responsibilities of Mines and Energy and Primary Industries and Fisheries.

[5] Another cabinet reshuffle on 4 February 2009 saw Vatskalis take the Government's Health portfolio from Dr Chris Burns while remaining the Minister for Primary Industry, Fisheries and Resources.