The State Department's senior official on European affairs came to one of the hotbeds of criticism of a new generation of NATO missiles today and charged that efforts to undermine the program strike at the foundation of the Atlantic Alliance.

Speaking at a conference sponsored by a foundation linked to West Germany's Social Democratic Party, Assistant Secretary of State for European Affairs Lawrence Eagleburger singled out those who have accused the Reagan administration of stonewalling on arms negotiations with the Soviet Union and who use this perceived U.S. hard line as one of the reasons to oppose the new NATO theater nuclear forces, known as TNF.

The left wing of Chancellor Helmut Schmidt's Social Democratic Party, along with a number of peace groups, is in the forefront of criticism of nuclear missiles modernization in West Germany, where the subject has become a dominant political issue that threatens to disrupt the alliance.

Eagleburger went straight to this possibility when he charged:

"I deeply regret the tendency among some to charge my country -- which has stood by Germany's side as a loyal ally and friend for 30 years -- with vicious and unsavory motives with regard to TNF. It is not we who poison the alliance with such wretched charges."

Eagleburger's speech at a U.S.-European conference on security issues for the most part refrained from attacking the motives of the peace movement. It appeared to be targeted at those, particularly among West German youth, who have opposed the NATO missiles plan and to reassure them of American good intentions. The language was some of the most direct used here publicly by an American official in some time.

"Should the alliance now retreat from its TNF commitment," Eagleburger said, "substantial and lasting damage could result." He listed a loss in Western credibility with the Soviets, and doubts among Americans about the commitment of the European allies. "Worst of all," Eagleburger said, "we would all be profoundly uncertain of our future ability to take difficult decisions together."

Eagleburger assured America's European allies that the Reagan administration intends to pursue arms control talks and build a "constructive relationship" with the Soviet Union.

"We have every reason to want a dialogue. Isolation of the Soviet Union is not our objective. Our aim is the resolution of specific problems standing in the way of better East-West understanding," Eagleburger said.

While stressing that talks will go forward, Eagleburger also urged the allies to stand firm on NATO's commitment to deploy 572 new medium-range nuclear missiles in Western Europe starting in late 1983.

The missiles represent NATO's most important concern at present. The decision to deploy them was made in 1979 to offset a buildup in similar Soviet weapons, and was coupled -- at the urging of the West Europeans -- to a NATO offer to the Soviet Union to negotiate limits on such weapons.

Eagleburger recalled that the decision to deploy the missiles as well came "at the invitation of our allies" in response to a perceived increase in the Soviet nuclear threat against Western Europe. It was intended, he said, to show again that the defenses of Europe and the United States are linked.

Addressing European fears, Eagleburger said, "This is not an act of cyncism. This is not an effort by the United States to make Europe a nuclear battleground."

He continued: "Our determination to modernize TNF is matched by our intention to carry through on our commitment to seek to negotiate TNF reductions with the Soviet Union. The president of the United States has pledged that he will negotiate; the secretary of state has made a similar pledge; the United States joined with its allies in Rome" in May in calling for talks by the end of this year.

"Against this background, ladies and gentlemen," Eagleburger concluded, "I for one am finding it ever more difficult to keep my patience when I am told 'the Americans don't want to negotiate' -- often by people who, I suspect, really mean: 'I wish the Americans would refuse to negotiate so that we need not carry out our commitment to deploy TNF.'"