The Mid Yorkshire Hospitals NHS Trust, which runs Pinderfields, said there were a "multitude of reasons" behind the waits and that it was trying to address the issue as a priority.
Hospitals across England are under huge strain amid further rises in coronavirus cases.
Pinderfields is currently treating 190 Covid patients, but Mid Yorkshire chief Martin Barkley said on Tuesday he was expecting that number to increase further over the course of the next week before any positive impact from lockdown kicks in.
The bed pressures are also causing delays in the hospital's Accident and Emergency (A&E) Department.
Mr Barkley said: "The number of people attending the emergency department Pinderfields on average is about 85 to 90 per cent of normal levels.
"Waiting times are long and in the main that’s because there's patients who’ve been admitted to hospital and are having to stay until a bed becomes available.
"Those waiting times have been poor, especially yesterday and today. It's poor for patients, it's poor for their families and it's poor for staff.
"That’s a key priority for us and we’re working on freeing up beds as best we can.
"The waiting times and pressures are not due to the people coming in through the front door. It’s the slowness out the back door of the hospital. That’s what’s causing the emergency department to be pretty full."
Mr Barkley said that among the reasons for the delays were the number of patients requiring treatment in single bedrooms.
He added: "As always with these things there’s a multitude of factors. If there was a simple answer, it would be straightforward to deal with."
But the trust chief stressed that he "did not want to discourage" people in need of emergency or life-saving treatment from coming to hospital.
The NHS has repeated its mantra that its open for business for those who need it, but has asked those not needing emergency help to be discerning about where they go to for treatment.
Mr Barkley said that attendance levels at Pontefract and Dewsbury Hospitals, both of which are also run by Mid Yorkshire, are "significantly lower than they were in this time last year".
To seek guidance on where to go for NHS treatment call 111. If you have a medical emergency call 999.
Local Democracy Reporting Service