Around 300 people are expected to be repatriated over the next two weeks.
The Secretary to the Prime Minister, Jimmy Rodgers, said the first flight from Brisbane would have 132 people on board.
He said another on Wednesday would bring 130 people from Fiji.
"Every country there is a second-phase of this virus going up," Mr Rodgers said.
"Instead of dropping our guard in this country it is now time for us to even tighten our guard further. Because now the reason is we are also looking at bringing our people home to safety."
Dr Rodgers said most of the people the government was looking to repatriate were Solomon Islanders stranded in Australia, New Zealand, Fiji and Vanuatu because of coronavirus border restrictions.
There will be some returning expatriates onboard the flights as well, he said.
A third charter flight is also expected soon to bring home workers from the Tuna industry.
Solomon Islands has had no confirmed cases of the coronavirus.