The claims - dismissed by Defence Secretary Malcolm Rifkind as "complete fiction"- centre on a dispute over whether the ports should be sold despite a lack of interest among potential purchasers.
Jack Dromey, the transport union's national secretary, said Mr Rifkind's personal adviser, David Hart, was at loggerheads with Roger Freeman, the defence procurement minister.
Mr Dromey's statement follows earlier reports, as saying an ideological struggle was taking place within the department over the sale of the forces' married quarters.
Interest in the sale of the two ports has been disappointing, with only the two managements bidding. The offer price is thought to have been very low, promoting suggestions that Mr Freeman feared the taxpayer was getting a raw deal.
Mr Dromey said: "Sources tell us that Hart has chastised Roger Freeman for not having the courage of the Government's privatisation convictions. A battle royal is raging in the MoD over the sale of the naval dockyards.''
Mr Hart , a former adviser to Margaret Thatcher, is well known for his right-wing views. Mr Freeman, however, is thought to be more cautious after his experience at the Department of Transport, where British Rail privatisation caused controversy.
Mr Hart told the Independent he had not discussed the sale with Mr Rifkind or Mr Freeman. "If Malcolm Rifkind asks me to look at it, I will. He hasn't yet.'' Mr Rifkind said the suggestions were laughable, "complete fiction.''