ITV News London has been told the club, which is ten points adrift at the bottom of the Football League, was meant to pay staff ten days ago but hasn't.
Last month, the club appeared in the High Court over an unpaid tax bill but avoided a winding up petition after chairman Francesco Becchetti settled the debt, understood to be in the region of £250,000.
The club, which is bottom of League Two, has other creditors and the hearing has been adjourned until June.
The club could be relegated on Good Friday if it loses against Luton Town and results elsewhere don't go their way.
It's not the first time players haven't been paid since Italian businessman Becchetti bought the club in 2014 from lifelong fan Barry Hearn.
Last week Omer Riza, one of the club's coaching staff, was named as the club's fifth manager of the season.
Leyton Orient has told ITV News London it is not making any comment.