Recent reports had suggested that Allegri was at loggerheads with the Dutch midfielder over a lack of starting action.
However, the coach has insisted that he has only had "normal" conversations with the veteran.
"There's no war between me and Seedorf," said Allegri.
"There are discussions in the changing room but that's normal, and there's no war with him or with any other player."
Milan are currently second in the Serie A table.