In a statement issued on Friday, the CFA said the current protocols would not allow for teams to properly prepare for games, which could lead to players being seriously injured.
"Our main concern from the outset was the health of all those involved, from footballers, technical staff of teams, and other employees at stadiums," said the CFA statement.
The championship was suspended on 15 March after Cyprus' first Covid-19 cases were reported.
The first division was at the play-off stage with another nine rounds of fixtures to go. Omonia Nicosia and Anorthosis Famagusta were tied at the top with 46 points each, champions APOEL were six points behind.
The CFA said ending the season would allow clubs, which have seen their balance sheets crumble, some breathing space to maintain their squads at a time when they have no income.