A new battle for control of the U.S. Synthetic Fuels Corp. is shaping up between the agency's controversial chairman, Edward E. Noble, and retiring Rep. Tom Corcoran (R-Ill.), one of three people recently nominated by President Reagan to the corporation's board of directors.

The immediate bone of contention is the selection of a new agency president, a post whose last two occupants, Victor A. Schroeder and Victor M. Thompson, were friends and former business asociates of Noble and were forced from office amid allegations of ethical improprieties.

Now, Noble has a new candidate to fill the $135,000-a-year job: Norman Callner, vice president for technical services of the Houston Natural Gas Corp. Noble has approved an interim contract that calls for Callner to serve as a $675-a-day management consultant until the newly reconstituted Synfuels board can meet and consider him for the top job.

But no sooner did Corcoran learn about this than he began raising conflict-of-interest questions about Callner.

The problem, according to Corcoran, is that Houston Natural Gas, through two of its subsdiaries, is part of a consortium that is seeking Synthetic Fuels Corp. funding for a coal-to-methanol project in Alabama.

In fact, Callner first came to Noble's attention because he was a member of the consortium's management group, agency sources say.

Speaking for Synfuels, Karen Hutchison said Callner would disqualify himself from any decision affecting the Alabama project. But Corcoran says he thinks it would be "virtually impossible" for Callner to insulate himself from the conflict problem.

"This is the kind of thing that the new leadership of the Synthetic Fuels Corp. should not tolerate," Corcoran said. "He would have direct management responsibility over all the people who are evaluating all the projects . . . . I think the continued insensitivity to these kinds of concerns on the part of a public corporation is something we're going to have to be wary of."

The conflict issue could well fade away quickly since Houston Natural Gas, according to a spokesman, plans to sell the two subsidiaries that are involved with the Alabama project within the next three to four months.

But agency sources say the real issue isn't Callner, it's control over the Synfuels program.

Sources allied with Noble believe that what Corcoran really wants is to snare the agency presidency, a not insubstantial plum for a congressman who will soon be lacking a full-time job. (Synfuels directors receive a part-time salary of $10,000 a year.)

Behind these concerns, however, is the larger issue of the synfuels program itself.

Repeated turmoil within the agency, combined with a worldwide oil glut that has undermined the economic logic of synfuels production, prompted Congress to chop $5.37 billion out of the Synfuels Corp.'s budget last month.

But the agency still has about $8 billion in government subsidies left to award and no clear consensus on how to spend them.

Corcoran has suggested the existing program needs to be "reevaluated;" Noble wants to push forward with many of the big projects now on the drawing boards and, as outlined in a recent budget memorandum, shut down the agency's Policy Development Group, which is involved in long-term strategic planning.

The outcome of this conflict should become clearer within the next few weeks, when the White House is expected to announce the recess appointments of Corcoran and the other two nominees to the board, economist Paul MacAvoy and energy executive Eric Reichl. This will allow the Synfuels board to meet for the first time since last April, when Thompson resigned and left it without enough members for a quorum. CAPTION: Picture 1, REP. TOM CORCORAN . . . soon to be underemployed; Picture 2, EDWARD E. NOBLE . . . has $8 billion to spend