Despite a phalanx of opposition from both sides of the Senate aisle, Commerce Secretary Malcolm Baldrige is pressing the White House to fill the top job at the National Oceanic and Atmospheric Administration with a man widely distrusted by NOAA's professional staff and whose scientific qualifications have been questioned.

Commerce spokesman B. Jay Cooper confirmed yesterday that Anthony J. Calio, now serving as deputy to NOAA Administrator John V. Byrne, is Baldrige's choice to take over the agency when Byrne leaves to become chancellor of Oregon State University next month.

"That's his recommendation to the White House," Cooper said. "My feeling is that he Calio has been a top manager . . . top-notch on every issue."

But a group of irate senators -- led by Commerce, Science and Transportation Committee Chairman Bob Packwood (R-Ore.) and the panel's ranking minority member, Sen. Ernest F. Hollings (D-S.C.) -- sharply disagree. If nominated, Calio would face confirmation hearings before the committee.

Hollings wrote Packwood earlier this month that he had checked all the panel's Democrats and "I have been assured that there is no support for him; all of our votes will be against him."

Opposition to Calio also has surfaced from another, more surprising source. In a letter to White House personnel director John Herrington in August, two of the Senate's most conservative members, Jesse Helms (R-N.C.) and Orrin G. Hatch (R-Utah), registered their support for a rival candidate, oceanographer James Baker of Princeton University, and warned that Calio has "alienated the scientific community in many important states."

Helms and Hatch said they could understand why Baldrige supported Calio, noting that many of the department's budget and personnel cuts had been shifted to NOAA because of Calio's failure to defend the agency's research budget.

Much of the criticism of Calio appears to center on his professional and scientific qualifications. While he uses the title "Dr.," Calio's only formal degree is a bachelor of arts in physics from the University of Pennsylvania. His doctorate is an honorary one, from Washington University in St. Louis.

Most of his professional career has been spent at the National Aeronautics and Space Administration, most recently as head of the U.S. civil space program. Calio came to NOAA from NASA in 1981.

Commerce spokesman Cooper said Calio's honorary degree was "no secret . . . . In the scheme of things it doesn't matter much." Cooper suggested that Calio's NASA background made him a very attractive candidate for the NOAA job, noting that "commercialization of space is a big initiative of this administration."

But in an Aug. 13 letter to Baldrige, Packwood and Hollings said they considered Calio's background in satellites "too limiting" for an agency whose scientific research responsibilities encompass a broad area of marine resources, meteorology, the environment and the atmosphere.

They also referred to "numerous controversies . . . which are attributable to and reflect upon Mr. Calio's abilities as a manager." While the letter did not elaborate on the "controversies," other sources said Calio has openly discussed his desire to dismiss several agency scientists said to be "disloyal" or too close to Byrne, the departing administrator.

Calio, who was in France on business, could not be reached for comment. But Cooper dismissed the allegations as routine agency in-fighting. "There has been some trench warfare, as in all the agencies around here," he said.

Other sources said the concerns of professional scientists at NOAA were heightened recently when Calio hired J. Roy Spradley Jr., formerly of the Interior Department solicitor's office, as a consultant.

The move was interpreted by some as an effort to tighten ties to Interior and the department's aggressive development policies. There also were some misgivings about Spradley, who got into hot water early in the Reagan administration when he quizzed a prospective Interior lawyer on his political affiliation and involvement in electoral politics.

In any case, none of the complaints has dissuaded Baldrige, who earlier this week asked Byrne to step down Oct. 15, a month earlier than his planned departure date, and take a temporary job as consultant to Calio, the new acting administrator.

Byrne was out of town Friday and unavailable for comment. But Cooper said he "told us he'd do whatever we asked him to."

White House personnel director Herrington, however, said he was unaware of any change in Byrne's plans. His resignation letter gave a Nov. 15 departure date, "and that's the letter we accepted," he said.

Herrington said no decision had been made on Byrne's successor. As for the controversy over Calio, he said: "I'm aware of it."