Mr Whale said the redundancies had put a lot of extra pressure on the remaining employee and while he was reluctant to "kick up a fuss" at this stage, he would be asking questions about why the trust had missed out on some of the $500,000 funding.
The trust had been full almost every night since January with people staying longer than usual.
"We don't seem to be able to get people into social housing as easily as we could last year."
Ministry community investment regional manager Nicole Devereux said the emergency housing sector played a key role in supporting vulnerable people.
"The $500,000 will go to 16 emergency housing providers who are contracted by the ministry to provide intensive social work services to vulnerable families in assisted emergency accommodation.
"MSD does not have a contract with Tai Tokerau Emergency Housing Trust at this time."
Funding arrangements with emergency housing providers were being reviewed because they were under more pressure from increased demand.
The additional $500,000 in funding had been allocated to relieve some of that pressure.