If you mean what Japanese call seiza, I would advise caution if you feel pain.
Despite studying martial arts for years, and doing daily stretching, I never could manage it. Things are made easier if you stretch the big thigh muscle (various techniques, including standing on one leg, holding onto your other foot, and gently stretching it up behind your buttock). Pain in the foot is sometimes also caused by contact with the floor, so a softer mat might help.
Knee pain is always worth paying serious attention to. I know several people who persisted in fighting joint pain in the interests of achieving flexibility, and who are now suffering for it. It might just be that some of us are not by nature meant to do this stuff!