The Environmental Protection Agency's inspector general has questioned the travel expenses and salary paid to an EPA official who investigators said had compiled a color-coded "hit list" for hiring, firing and transferring agency employes.

The inspector general's report said that W. Clifton Miller, who works in the office of the EPA administrator, charged the government $22,058 in travel expenses over the past two years, and that most of it was for rent on his Virginia apartment while he traveled out of town on EPA business.

The inspector general noted that the travel expenses had been approved by Miller's superiors, but said that $2,473 of the charges were "improper" on technical grounds and should be repaid.

In addition, acting inspector general Charles L. Dempsey said that Miller's salary increased over the past two years from $38,456 to $63,115 "through a series of unusual personnel actions." Miller, who was close to former EPA administrator Anne M. Burford, also received a $5,000 cash bonus at Burford's request, the report said.

Miller could not be reached for comment, and an EPA spokesman said that the agency would not comment on a personnel matter.

Rep. Patricia Schroeder (D-Colo.), who requested the report, said the findings are an example of the "mismanagement and political opportunism that has marred the agency during the Reagan administration."

Dempsey asked acting EPA Administrator Lee Verstandig to drop plans to make Miller the agency's assistant regional administrator in Denver, saying that the findings "raise serious questions about Miller's ability to perform in his proposed position."

In a separate letter to Schroeder, Dempsey said that a list of senior executive service managers at EPA "was prepared and maintained by Miller to be used in personnel decisions involving these employes." He said the list "allegedly identified employes by a color code which may have been based on their political affiliation."

Investigators said that the list, which was found on Miller's wall and was one of several "hit lists" discovered at the agency, apparently was used as a guide to firing or transferring several career employes. Dempsey has asked the special counsel of the Merit Systems Protection Board to investigate whether Miller's use of the employe list violated civil service rules.

Miller was a GS-13 management analyst in Denver when he was temporarily detailed to Washington in April, 1981. With Burford's help, he then received a series of seven temporary reassignments that gradually boosted his salary to $63,115, the report said. While these raises were not illegal, the report said, only one involved a merit promotion.

Miller remained on "temporary" status in Washington until this month, although he had moved into a Virginia apartment with another EPA employe, investigators said. Miller submitted vouchers for the daily cost of the apartment whenever he traveled out of town, the report said.

According to the report, Miller told investigators that "it was determined to be overall less costly to the government for him to maintain an apartment at a monthly rate than for him to occupy and pay for short-term hotel lodging when he was in D.C."