ABDA suspected the presence of Japanese carriers, an imminent invasion of Timor and a support fleet lying in wait and thus ordered the convoy back to Darwin which it reached before noon on 18 February.

[4][5][6] Warrego was in Darwin the next day when the Japanese attacked the port and, though with a working party over the side, was one of the ships that got underway to contribute antiaircraft fire to the defense.

With HMAS Ballarat, Warrego escorted Karsik and Dutch ship SS Bontekoe in the first convoy into Milne Bay on 25 June 1942 with Australian troops, American engineers and supplies for the buildup of that base in preparation for port operations and airfield construction.

[8] By 11 July, the sloop was back, escorting the Dutch ship SS Tasman with Brigadier John Field and the 7th Brigade Group embarked as Milne Force to protect airfields under construction.

[9] By late October Warrego, HMAS Stella, and HMAS Polaris were assisting the survey vessel Paluma in surveying a safe passage for large ships from Milne Bay to Cape Nelson in order to provide large ship support to the Buna campaign that led to Karsik delivering tanks to Buna and the supply convoys of Operation Lilliput.