The Department for Transport (DfT) announced funding worth a total of £4.3 million for the public service obligation (PSO) routes.
Cornwall Council will receive up to £1.8 million to run flights between London and Newquay.
The route was operated by Flybe until it went bust in March 2020.
Flights from Cornwall Newquay Airport to Gatwick Airport will be operated by Eastern Airways from December 9.
British Airways launched summer operations between Newquay and London Heathrow last year.
The PSO means flights will operate throughout the year.
The DfT also confirmed it will provide £2.5 million to keep direct flights between Dundee and London running until 2023.
Loganair will continue to run the flights from Dundee Airport to London City Airport.
Aviation minister Robert Courts said: “We’re maintaining these vital transport links, including the hugely popular London to Dundee and the reinstated Newquay to London routes, for people right across the country for tourism and business travel.
“The Government is fully behind UK regional connectivity and strengthening these routes as we build back better from the pandemic.”
The Scottish Government’s transport minster Graeme Dey said: “I welcome the extension of this contract which will continue to provide important connectivity for Dundee.
“This service will benefit business travellers and offer visitors a direct route to experience the tourism offering in the city and surrounding area.
"The Scottish Government is committed to continuing to support the service both through our direct contribution to the cost of the flights and our ongoing subsidy of Dundee Airport.”
Philip Desmonde, Cornwall Council cabinet member for transport, said: “It is vital for our residents and business community that direct flights between Newquay and London are maintained, and I welcome the news that Eastern Airways will operate our key route.
“This PSO service not only protects Cornwall’s links with London but also offers excellent connectivity around the world into the future.”
Richard Hill, chief commercial officer at London City Airport, said: “Connecting all parts of the UK to London has always been core to our business and we are delighted that the service to Dundee has been extended for another two years.”