The report also said the additive caused cancer, though the ministry said it was noncarcinogenic.
The incident sparked anger and panic among Israeli consumers.
"Milk is a very sensitive issue," Labor Knesset member Yoram Lass, also a former Health Ministry director general, told Israel Radio. "No one can take chemical stuff" that is used either to prevent foaming or clean pipes "and put in into our milk."
Tnuva took out large ads in newspapers in an effort to dispel fears. The milk manufacturer also pulled its products off store shelves.
On Sunday, Tnuva's director general Yitzhak Landesman admitted that the silicone had been added to the 1 percent milk as an anti-foaming agent. Earlier, Tnuva denied using the additive in its milk, saying that a silicone agent was safely used to clean machines at one of their dairies, in Rehovot.
Landesman also denied that the company had originally lied about using silicone. But he said the director of the Rehovot dairy would be suspended.
Health Minister Ephraim Sneh told Army Radio that the tests carried out by inspectors do not identify the silicone compound.
"The agent is used as a preservative in many foods, but not in milk," Sneh told Army Radio. "The checks are for bacteria, toxic substances and nutritional makeup."