Following a positive Covid-19 case in the Clyde squad, the Fifers decided it would be unsafe for their players to compete.
Boss Darren Young confirmed afterwards that some of his squad have partners who are pregnant while others were concerned for their employment should they be subject to a period of quarantine through the track and trace system.
The club has been roundly praised for its position.
However, league chiefs said on Wednesday that the SPFL would be investigating the matter further.
A statement said: "Following the call-off of the SPFL League 1 fixture between Clyde and East Fife last night, the SPFL has today (28 April) announced that disciplinary proceedings have commenced against East Fife for failing to fulfil the fixture.
"The disciplinary hearing will be held before a sub-committee of the board of the SPFL on Thursday 29 April."