Senate Republican leader Howard H. Baker Jr. (Tenn.) said yesterday that he had been prepared to support the natural gas compromise bill but reports that President Carter linked the legislation to concessions on nuclear breeder reactors had "muddied the waters."

"I very much hope I can support that bill because I think we need an energy policy," Baker said on "Meet The Press" (NBC, WRC). "But the waters have been muddied now, and until I can see to the bottom I won't know."

Carter reportedly made an agreement with Sen. James McClure (R-Idaho) in exchange for his approval of the natural gas conference report. McClure's signature was needed for the bill to return to the House and Senate for final voting.

McClure, after a Thursday night meeting with Carter, said he had reached an agreement with the president to "establish a basis for a breeder program." Carter has opposed breeder reactors because of the large amounts of radioactive plutonium waste generated.

Baker favor a breeder program but fears the McClure-Carter deal could hurt Tennessee.

"While the agreement seems to commit the administration to the development of a breeder reactor, it would imply the cancellation of the breeder reactor project in my state, and that hardly seems like a good deal to me at this moment," Baker said.

He added that he understands the McClure-Carter arrangement would halt work on the Clinch River breeder reactor program in Tennessee and would give Carter the right to cancel Clinch River after 1981.

Clinch River is the only breeder project under way, but Idaho - represented by McClure - had a small, experimental project begun in the early 1950s. If Clinch Rivers is canceled, Idaho and other states have been mentioned as possible alternative sites.

Baker said that neither McClure nor anyone from the administration informed him in advance that the breeder reactor might be linked to the natural gas bill.

Before learning of the concessions on breeder reactors, Baker said, he had called Carter to announce his intention of supporting the natural gas compromise.

Shortly before Baker's statements on the natural gas bill, Energy Secretary James R. Schlesinger Jr. said on "Face the Nation" (CBS, WDVM) that he believes the compromise will be passed.

The administration had reserve votes for signing the conference report in case they were needed, he said, and despite opposition "I think that we will get it out of Congress."

Should the natural gas bill fail, however, and Congress refuse to pass a crude oil tax to reduce imports, then "I think that we can confess that we do not have the discipline in this country to face up to our energy problems," Schlesinger said.

If no energy legislation is passed, Schlesinger said the president could be forced to impose "very unattractive" quotas or tariffs to reduce oil imports.

Schlesinger said that his position as energy secretary was not dependent on getting an energy program passed by Congress, but "if it becomes clear that we are unable to have such a program then my usefulness may have ended."