Concerns were raised after councils said that the flagship policy was undeliverable because of a funding shortfall of nearly £25 million.
The Scottish Government's move to feed 165,000 young Scots in their first three years of school has been backed by £64m in public funding, but councils say the true cost could be as much as £88m.
John Dickie, head of the Child Poverty Action Group in Scotland, urged councils and ministers to work together - but he also called for legislation to ensure the policy was delivered.
"It would be a tragedy if the benefits of a free healthy lunch were to fall victim to funding disagreements," he said.
"It's now crucial that the commitment made by the First Minister is backed up by a statutory entitlement to a healthy free school lunch in the early years of primary.
The call comes just weeks after First Minister Alex Salmond announced all pupils in P1 to P3 would get a free lunch from January next year.
Mr Salmond said the move was worth £330 a year per child to families.
However, Cosla, the umbrella body for councils, said the government had underestimated take-up.
A Scottish Government spokesman said: "To deliver our commitment on free school meals, we have been working closely with Cosla and to explore how any practical implications can be addressed; building on the experience of the free school meal trial over 2007-08."