Those affected are missing additional pay for working unsocial hours. The trust said all staff had received their basic pay.
It said the error was due to a software problem in a payroll feeder system.
SDLP councillor Nichola Mallon said some people had been underpaid between Â£200 and Â£300 in October.
She said there had been a number of errors since the "multi-million pound" system for payments was introduced in 2013.
"Between October 2013 when it was first introduced, and May 2014, in the Belfast Trust alone they had to make 3,002 additional corrections to pay," she said.
"People have had wrong National Insurance contributions deducted, many of them were awarded tax rebates that were subsequently taken back off them.
"You fast forward two years and here we are again.
"We need to have a serious look at this problem.
"The staff who are affected are those working the most unsociable and stressful hours on the front line, being underpaid, now they are having to chase up to get what is entitled to them."
The trust said staff would receive their outstanding payments on Tuesday.
It said it would engage with the system providers to investigate what had happened to ensure there was no repeat in the November payroll.
"We would encourage staff to contact their line management if they have any concerns," it added.
Almost 1500 workers employed by the Belfast Health and Social Care Trust have not received their full pay this month.