Tourist visa extension

Hi, I'm on a visa waiver and my flights home have just been cancelled. There are still 3 flights a week on ANA but they are very expensive so I would rather just stay here til cheaper flights start up again. I am wondering if anyone has been able to get a 90 day extension while there are still flights to their home country?

You need to go to the immigration office.
Make sure you do before your visa expires, if you overstay you have another problem.

You can explain immigration and you may have to fill in a application.

http://www.moj.go.jp/content/001316300.pdf

Currently the Ministry of Justice is allowing those staying in Japan with resident status expiring in March, April, May, or June but "cannot leave" due to the pandemic situation to apply for extension 3 months beyond the original expiry date so as to reduce the congestion at the immigration bureau. (This is the latest as far as I know (dated April 3), but please check the MoJ�fs website for any update.)

But whether not paying for an available (but expensive) flight counts as "cannot leave" is a question, so if I were you, I'd phone the immigration bureau.

I doubt that any less expensive flight will be available any time soon though.

Yup. It is gonna be more than 90 days for cheaper flights to kick in. Prices returning to Jan/Feb 2020 prices will be a two or three year recovery.

To give some food for thought.

I'm currently living in Singapore but am not allowed to leave until mid June due to contractural obligations. I've been recording the number of international flights each day from 10 Asian major airports for over 3 weeks to look for trends.

Yesterday - there were 6 international flights from Haneda, 14 from Narita, 5 from Sydney, 16 from Singapore and 55 from Hong Kong. These numbers have continued to lower over the past 3 weeks.

My question for you would be not if you should wait for a cheaper flight - but will there be a flight to catch?

Can you not afford the flight, or do you just not want to pay for a more expensive flight? There is a big difference.

Do you have travel insurance? Can you get your flight changed at no cost with their assistance?

flights home have just been cancelled
Really, just now? Most flight changes and cancellation occurred weeks ago.
As for flights within the next 90-days, Immigration will not have any sympathy for you if you're still here in three months and chose not to take an available flight. I am surprised that the cost of staying in Japan is lower than the likely cost of a replacement flight.

As long as flights go you need to go back. There is no consideration of the immigration with the price.
If you overstay you will have bigger issue than the cost of the flight.