More Assertive Bonn Strains Ties With US. Delay on missile modernization is latest friction point. ALLIES AT ODDS

CHANCELLOR Helmut Kohl's recent call for a delay in deciding about the modernization of the West's short-range nuclear missiles has jolted the Western alliance. United States Secretary of State James Baker III, in Bonn as part of a tour of NATO capitals, is trying to play down the issue. But Mr. Kohl's move is seen by diplomats based here as the latest friction point between the US and West Germany as Bonn asserts itself in ways unheard of only a few years ago.

In recent months, the US and West Germany have wrangled over US beef exports to the Common Market and West German chemical sales to Libya. At the same time, West German public opinion is shifting in directions that trouble US officials.

West Germany remains one of Washington's staunchest allies. It hosts nearly 1 million NATO troops and contributes heavily to Western defenses. Chancellor Kohl was the first Western leader to get a telephone call from President Bush after the inauguration - evidence of Bonn's central role in US foreign policy.

But West Germans are increasingly voicing their objections to the large foreign military presence in their country. Opposition to low-level flight training, once the province of environmentalists and peace activists, has developed into a grass-roots movement, centered in some of the most conservative regions of southern Germany. Over 60 percent of West Germans would now ban such flights.

Against this background, the West German desire to put off missile modernization is seen by some critics as further evidence of the eroding military consensus in West Germany.

Most of the West's arsenal of short-range nuclear forces - those with a range of less than 500 kilometers (300 miles) - are based in West Germany. So Bonn's cooperation is considered central to any modernization plan.

Plus, timing is crucial.

NATO's aging stockpile of short-range Lance missiles, with a range of 110 kilometers (66 miles), are due to be replaced in 1995. The US Congress has insisted that it will not appropriate money for a large-scale replacement program unless there is an allied commitment to support the initiative. Last year's Pentagon budget carried enough money to do the preliminary studies.

``The question now,'' says one US State Department official, ``is what Congress will require to carry this over and make it a larger item in the coming year.''

Congressional leaders emphasize that this is more than a question of money. Support for joint military planning is considered a crucial element of ``burden-sharing'' within the alliance.

West German officials say Kohl's stance - that the decision on modernizing the missiles can wait at least two years - was prompted at least partially by recent Soviet and East European pledges to unilaterally cut conventional weapons. One faction of the Bonn government - led by Foreign Minister Hans-Dietrich Genscher - has long argued that an early decision on modernization might send the wrong signal to the East, possibly even scuttling East-West d'etente.

But the key to the West German position is domestic politics.

Modernization is unpopular in West Germany, where nearly 80 percent of the public now say they want all nuclear weapons removed from Europe. Short-range weapons are especially unpalatable among West Germans, since their range means that they would be used primarily on German territory, East or West.

Kohl wants to avoid a repetition of what happened in the early 1980s, when NATO installed a new generation of intermediate-range nuclear weapons in Europe. The so-called two-track decision, in which the West deployed the weapons while also negotiating their elimination, sparked an unprecedented outpouring of public opposition.

There's a serious question about whether Bonn's ruling center-right coalition could survive such an uproar over short-range weapons.

Last month's election in West Berlin - in which a tiny far-right party was able to lure away many dissatisfied conservative voters - has rattled the Bonn government and added to a growing series of embarrassing losses in state elections. By putting off modernization, the chancellor hopes to avoid giving his opponents more ammunition to use against him in general elections slated for the end of 1990.

Until now, it was assumed the allies would settle the issue at a NATO summit slated for later this spring.

The alliance is preparing a ``comprehensive concept'' which spells out NATO's strategy for disarmament. The document was expected to endorse modernization formally, while wrapping it into a larger context of arms cuts. ``The only way you can address modernization in Germany is not as a single topic,'' says the State Department official. ``If you do, it's a loser.''

Kohl has said he still thinks the document can be finalized in coming months. But the result now, say analysts, is likely to be an extremely vague outline. This is ironic, since in many ways the ``comprehensive concept'' had become a vehicle for making modernization politically acceptable in West Germany.

Meanwhile, the West German leader is careful to emphasize that he's not opposed to the eventual modernization of the weapons. A spokesman for the Bonn government said over the weekend that the West Germans wanted to keep options open.

The key question now is how the alliance will deal with the issue in coming months.

Most analysts do not expect the US to lean very hard on West Germany - recognizing that a politically painful decision now could backfire later in the form of greater domestic instability inside West Germany.