The Zoo Animals Fund was created by the government to help zoos facing financial trouble in the pandemic with £100m available.
In a letter to the Prime Minister, the British and Irish Association for Zoos and Aquariums (Biaza) says the fund has "failed to provide" adequate support.
It claims many zoos are unable to access the money.
Out of 300 licensed zoos, 34 have been awarded funding, with a further 23 applications being processed.
Biaza says this makes up £6m of the £100m available and major wildlife attractions such as London Zoo remain ineligible for help.
Zoos are currently shut in this lockdown.
"That is why we have set up the Zoo Animals Fund on top of the other support available - to ensure that those facing severe financial difficulties can continue to provide the best possible care for their animals."
Zoos need to be 12 weeks from bankruptcy to qualify and by that time any responsible animal park would already be trying to find new homes for its residents, Biaza says.
The pandemic has been a difficult time for zoos, which have lost a lot of income due to fewer visitors.
Jamie Mainds is a senior zookeeper at Chessington in Surrey and says it's "business as usual" when it comes to the care of animals.
"The main difference is we've got no guests to educate, inspire and engage with these amazing animals we have," the 27-year-old tells Newsbeat.
He looks after birds, sea lions and mammals such as meerkats and bearcats and says animals "learn to adapt" to the environment they're in.
Jamie says the gorillas have picked up on the change and have been interacting more with one another compared to when the public is able to come in.
He adds that the youngest gorilla has been able to spend more time playing with her aunties, uncles and cousins.
You might have seen the videos of penguins in the US roaming around zoos and aquariums, and Jamie says there is a greater "freedom of time" for animals and zookeepers now.
And Jackson the bearcat "absolutely loves" the extra time.
"He's only recently seen snow for the first time and it's been absolutely fantastic. We took him down to the gorilla view and it's fantastic for them too.
"It's enriching to go to different locations, environments and pick up different smells and sounds."
Jamie says zoos such as Chessington are vital for the animals.
"We're part of breeding programmes so the animals we have here are playing that part to having a backup generation in case species in the wild do go extinct."
He adds: "We're more than just an attraction for people to come and look at animals. We're trying to help species survive."
From the end of February, zoos will no longer be able to apply for the Zoo Animals Fund.
In the letter to the Prime Minister, Biaza say it's vital the remaining £94m "is ring-fenced for the creation of an accessible Zoo Recovery Fund".
Nicky Needham, acting director of the charity said: "We must see the ineffectual Zoo Animals Fund replaced so that zoos, aquariums and safari parks large and small get the support they need to survive, thrive and fight extinction."
The Defra spokeswoman added the existing scheme has "offered a vital lifeline to ensure the continued welfare of zoo animals.
"We continue to process applications to support the sector during this challenging period. We would strongly encourage any zoos in need to apply to the fund."