The Reagan administration's chief antitrust officer yesterday said he found Mobil Corp.'s effort to buy control of Conoco Inc. "troublesome," because of the "potential competition problem" the merger might have created.

Assistant Attorney General for Antitrust William Baxter said he was not particularly concerned about the size of the two companies. He said he was concerned that the two companies are competitive today in many markets in a changing industry, "with the prospect that over the years immediately ahead, they would be thrown into competition with one another" in new markets.

"That is the sense in which a Mobil-Conoco type merger is troublesome, apart from the horizontal problems one can presently perceive," Baxter said.

For now, Baxter said, he has told the Justice Department Antitrust Division staff not to continue to study 30 boxes of documents obtained from Mobil in connection with their investigation of the takeover proposal, since from all indications E.I. du Pont de Nemours & Co. has won the bidding war for Conoco.

"As a consequence, I cannot tell you whether we would have approved it or not," he stated. Baxter said he has also told other oil companies that they need not respond to earlier requests for industry data related to the Mobil bid.

Baxter said he did not think administration antitrust policy had set off a wave of mergers. But he said he is "alarmed" by difficult management problems posed by possible large numbers of premerger notification notices being filed. "Where I'm going to find the staff to process them, I don't know," he said.

He said the administration has not "introduced uncertainty" into antitrust matters, but added that business representatives would have to rely on recent merger case law for policy guidance.

To alleviate that situation, Baxter said he is revising the 1968 merger guidelines, which he said "have not, in fact, been followed by any administration over the last eight years at least. The private bar did not take them seriously. Everyone knew they did not reflect the enforcement intentions of the division." The new guidelines could be ready by winter, he said.

In the meantime, the department's policy on horizontal merger cases, or those in which companies buy their competitors, would be similar to policies spelled out in the cases brought in recent years by the Justice Department. On vertical mergers, those involving purchases of companies that supply a piece of the chain of production, for example, and on conglomerate mergers, the department's policy would change drastically.

"Mergers are never troublesome except insofar as they give rise to horizontal problems, so that the vertical merger guidelines, as far as I'm concerned, just disappear," said Baxter, a former Stanford University law professor.

On other matters, Baxter said the objectives of the government's antitrust suit against American Telephone & Telegraph Co. "would largely have been achieved" if Congress adopts telecommunications legislation with two amendments he is preparing. If the legislation was "pretty well along," he would recommend the suit be dropped, he said.

Baxter, who had charged in the spring that the legislation would undermine the case and create added layers of regulation, said he changed his position because "a legislative solution is attainable with a high degree of finality" and because the legislation would get rid of the "uncertainty and escalating capital costs" in the communications field.

One amendment is designed to ensure that AT&T's local phone companies are not paying too much for equipment purchased from AT&T's Western Electric Co., a problem that could cause "below-competitive-cost pricing," he said. The second would put competing long-distance carriers "in the same relationship with respect to local telephone companies that is enjoyed" by AT&T's long-distance division, he said.