The first new American medium-range missiles to go operational in Europe late this year may be ground-launched cruise missiles based in England rather than those based in Italy or the more controversial Pershing II ballistic missiles in West Germany.

A delay in putting the Pershing IIs in place could complicate political problems in the European countries, but also might increase opportunities for Soviet-American missile negotiators in Geneva.

The slower cruise missiles are considered less of a threat to the Soviet Union than the Pershing IIs, whose warheads could hit targets inside the Soviet Union within 10 minutes after being launched from West Germany.

The first nine Pershing IIs, now scheduled to arrive in West Germany by mid-December, may not become ready for action until March, the same time that cruise missiles are expected to go on alert in Italy, according to Pentagon and Capitol Hill sources.

That would mean that 16 cruise missiles based at Greenham Common, England, scheduled to go on alert in December, would be the first new nuclear medium-range missiles to become operational.

But a top Defense Department official said yesterday that the four NATO nations have been negotiating for several weeks to close the gap in operational dates.

The Pershing II delay stems in part from technical problems with guidance system maps.

But some sources said it also results from an agreement between the Carter administration and the government of former West German chancellor Helmut Schmidt to link the initial operational date of the Pershing IIs in Germany to that of the cruise missiles in Italy.

Earlier this year, Air Force Secretary Verne Orr told a closed session of the House Appropriations defense subcommittee that the cruise missiles scheduled for Comiso, Sicily, will not be operational until March.

"The Italian government was very late in giving us permission, naming what piece of land we could have and giving it to us," he said. "And when we got it, it was worse than vacant land. It had buildings on it that had to be torn down."

A declassified version of Orr's remarks was published recently, and yesterday an Air Force official said March is still the target date for Comiso. "Even then," he added, "it will be a bare base operation."

Officially, however, spokesmen for the State and Defense departments yesterday maintained that there would be no delays in the operational readiness of the missiles in any of the three countries. And other sources said the Schmidt agreement has not been endorsed by the Kohl government.

Any acknowledged slippage, one administration official said, could lead to increased political problems in the host countries.

As a result of the current conversations, a Defense Department official said, ways are being found to have the missiles in England and some in West Germany operating in December, with the first few in Italy following shortly thereafter.

"We now expect them to take place with near simultaneity," he added.

Other officials involved in the deployments or briefed recently about them are not so certain.

The need for highly accurate maps required in the Pershing II's terminal guidance system cannot be fulfilled overnight, sources said. And while the missiles could be installed on West German bases, they would not be 100 percent operational by Army standards.

The Schmidt agreement with the Carter administration was based on the former German leader's belief that West Germany could not be the only non-nuclear continental European power with an operational nuclear missile on its soil that could hit targets in the Soviet Union.

"The British will go first and alone in December," a Pentagon official said earlier this week.

But he pointed out that, during the fall and winter, equipment, men, material and the nuclear warheads will be sent into West Germany for the Pershings and to Sicily for the cruise missiles to support the March operational target dates.

A brief, built-in delay in the Pershing operational date, one source said, would offer additional time for Soviet-American negotiations in Geneva early next year after one set of cruise missiles had become operational but before the more controversial Pershings went on alert.

However, one official close to the American program said the consensus in the Reagan administration now is that "one-third to one-half" the planned 108 Pershings and 464 cruise missiles will have to be deployed and operational in the next two years before some agreement will be reached.