The Reagan administration's decision to put cruise missiles aboard submarines will provide "some ammunition" to European critics of earlier NATO plans to base U.S. cruise missiles on European soil, the American commander of NATO forces said yesterday.

The commander, Army Gen. Bernard Rogers, said in effect that the decision was helpful from the standpoint of showing U.S. resolve, gaining strength for any future arms control negotiations and complicating the life of any would-be Soviet attackers.

But speaking as the commander of the NATO alliance, he said the decision "causes me a little bit of concern" because it could "fuzz up" the distinction between tactical and strategic nuclear weapons and will provide more ammunition to those in Western Europe already critical of another key NATO plan. Under that plan, agreed to in 1979, U.S.-built Pershing II missiles and cruise missiles would be deployed in England, West Germany, Italy and possibly Belgium and the Netherlands.

"I carry water on both shoulders" on this one, Rogers said.

The decision to deploy "several hundred" nuclear-armed cruise missiles aboard U.S. attack submarines is one of the less-publicized aspects of the $180 billion strategic weapons program unveiled by President Reagan last Friday.

The idea, as explained by the White House, was to use the missiles to help plug any gap in the nuclear balance with Moscow. The missiles would serve as a "strategic reserve force" and as a deterrent to attacks on U.S. naval forces.

The potential problem, however, is that Washington has been pressing the West Europeans not to back away from the 1979 missile-deployment plan, which was intended to offset hundreds of new Soviet SS20 missiles already deployed.

There is, however, considerable political opposition to such deployments, especially in Germany, Belgium and Holland. The concern now is that the new U.S. decision to put other cruise missiles on submarines will make it easier for critics to argue that the European missiles also should be at sea.

State Department officials yesterday also acknowledged that the recent decision probably will cause some problems in European public opinion.

At a breakfast meeting with reporters, Rogers was supportive of Reagan's determination to beef up all U.S. strategic forces. But well into a lengthy question-and-answer session, Rogers said, "Obviously, you can see I'm somewhat concerned" that some things "thrashed out" in previous years with European foreign ministers might have to be gone over again "as a consequence of the announcement of Friday."

"We have always, in the past, maintained that if you put cruise missiles witrh nuclear warheads on submarines you are, in fact, fuzzing up the distinction between tactical and strategic nuclear weapons" launched from submarines, which can carry both, he said. This ambiguity could be avoided by keeping cruise missiles on land, he said.

Rogers maintained that the Europeans needed to stick to the land-based scheme to show European resolve, alliance cohesion and to share the nuclear risks with the United States.

Without being critical of the specific new presidential plan, Rogers said that "anything that diverts attention" from the 1979 NATO plan "is not helpful."

He added that the presidential announcement in August on assembly of neutron warheads for U.S. forces also was a source of considerable political controversy in Europe, even though the weapons are to be stored in the United States. European critics see them as fitting into a pattern of new U.S. weapons and policies that suggest war in Europe is becoming more likely, he said.