An internal probe has been launched by the Scottish Association of Mental Health, which has blamed the problem on an "electronic glitch".
The Glasgow-based charity offers nationwide support services along with a range of programmes and employs more than 700 staff.
But charity chiefs last night admitted that "several hundred" had not received their monthly pay due in bank accounts yesterday.
They launched an immediate investigation and are working closely with the banking sector to identify the cause of the problem.
The organisation's finance department handed out cash to affected staff with the promise the "manual part payments" would be followed up with full payments placed in personal accounts over the weekend.
A spokeswoman for the charity, based in Wyndford Road, Maryhill, admitted a "significant number" of staff had been affected.
She said: "There has been a technical issue. Everything is being done to rectify the problem. We are extremely concerned for our staff.
"They are a priority. We are making part payments to them and have promised to have the rest of their wage in their bank account before the end of the weekend.
"Naturally, we are sorry this has happened."