KidsCan says it's been told it will lose its funding on 30 June next year.
The charity feeds 30,000 children a week across 700 New Zealand schools.
Its executive Julie Chapman told Checkpoint last night KidsCan provides 30,000 pairs of shoes, 50,000 pairs of socks, and 40,000 raincoats a year.
Ms Chapman said Oranga Tamariki told her the $350,000 would not be renewed on July 1, 2018.
However, the Minister for Children Tracey Martin said the charity's funding was always time-limited and would be up for assessment.
"My understanding is KidsCan knew it was always a time-limited fund. The National government never did any future projections for it and so we're going through a budget process."
Ms Martin said there were never any guarantees of funding and continued financing is part of the budget process.
"There are a huge number of partnerships that Oranga Tamariki is involved with for the benefit of children. I can't do negotiations around their contracts based on a television or radio programme."
"I have to make a budget bid to the government in the same way and other government before me has had to do."
Ms Martin said she would have preferred Ms Chapman had spoken to her rather than talking to John Campbell.
"KidsCan does amazing work, but with every single one of the dollars we provide I need to make sure we can justify the spend based on figures, not on a television programme."
Ms Chapman told Checkpoint that if the charity lost funding, there would be a big impact on its ability to get support to kids in need.
"If this funding does go ... children are going to go hungry, they're going to have to wait longer without clothing, without shoes, all those things that they're in urgent need of."