In a letter seen by the Weekly, the council has told proprietor Trish Burke to stop using the premises as an animal shelter because she is in breach of the planning scheme and the business is unregistered.

Ms Burke has applied for re-registration for the shelter, but the council says she needs a planning permit before the application can be approved.

The council has given Ms Burke until February 29 to comply with the order.

But she has been told to respond by tomorrow. Failing this, the application would be refused and the shelter will be closed.

The shelter was shut by the council in December 2010 because of overcrowding and incomplete paperwork.

Ms Burke was thrown a lifeline by the council a month later and allowed to reopen with a temporary planning permit.

She claims the council failed to advise her when the interim permit expired.

Last month, the shelter was placed on a 11-day ban because of permit breaches.

In the letter, the council said it had been wrong to issue a temporary permit.

Ms Burke told the Weekly last week she had been "tortured" by the council since opening the shelter in 2009.

Lawyer Kurt Falkenstein, acting on behalf of Ms Burke, said he was investigating taking the matter to VCAT and the Victorian Ombudsman.

Council director of assets and operations Dale Thornton said on Friday evening he was waiting for Ms Burke's reply.

"We do recognise the importance of her work in assisting animals and recognise it is a valuable service."