Agriculture Minister Jaala Pulford announced via Twitter on Wednesday night that her department would investigate growing community concerns about the practices and animal management at the Lost Dogs' Home in North Melbourne.

Ms Pulford said she had been shocked by stories from people who claimed their dogs had been wrongly put down at the centre, which provides pound services for 13 council areas in Victoria.

Earlier this week, it was reported that a widow's pet dog, Fonzie, was put down by the Lost Dogs' Home the day after his owner had called to claim him.

Ms Pulford said she had been inundated with phone calls, emails and messages on social media from people expressing their concern. She said she had also been contacted by former staff at the Lost Dogs' Home.

"That's why we've asked for this investigation," she told radio station 3AW on Thursday.

One of two online petitions calling for an investigation into the shelter attracted nearly 10,000 signatures, with many people expressing concern about high euthanasia rates, the identification of owners of animals, accommodation and housing of animals, and the assessment of animals for re-homing.

The petition organiser, Kae Norman, of Rescued with Love, said she had been working to highlight concerns about the shelter for the past decade.

"I think there's been a lot of convenience killing," Ms Norman said.

She said the shelter had previously put down dogs deemed to be "too exuberant" and others with minor medical conditions.

Melbourne City Council severed its 14-year relationship with the shelter in 2013, letting its $450,000 contract lapse, despite having an option for a three-year extension.

Chair of the Lost Dogs' Home, Dr Andrew Tribe, said the shelter would review its policies and practices and aim to create a "more transparent, co-operative and compassionate approach".

"We want to continue to reduce the numbers of animals put to sleep, through increasing adoption and continuing education and outreach programs to reduce abandoned and lost animals," Dr Tribe said in a statement.

He said the shelter would also appoint a dedicated rescue co-ordinator.

"We want to throw our doors open to those rescue groups who are best placed to help us. We are increasing our behavioural resources to further develop our animal assessment and rehabilitation."

Dr Tribe defended the organisation's reported handling of the widow's dog, Fonzie.

He said Fonzie was held at the shelter for 10 days, despite not having a tag or a microchip. He said the owner contacted the shelter on the ninth day, which was a Sunday, just before closing.

By the time the owner was able to visit the shelter, Fonzie had been put down.

"We strive every day to treat every animal in our care with compassion and always work towards the best possible outcome for them," Dr Tribe said.

"Sadly, in animal welfare organisations like ours, not all the animals that we receive are either able to be rehabilitated, or will be adopted. That means part of our role is the humane euthanasia of animals."