MIAMI (AP) _ A federal grand jury is still investigating Bahamas Prime Minister Sir Lynden O. Pindling, but the case of Panama's Gen. Manuel Antonoio Noriega may stand in the way of an indictment, a newspaper reported Monday.

The shaky status of federal drug indictments in Miami and Tampa against Noriega has raised doubts about whether the United States would want to indict a foreign head of state. The Reagan administration reportedly has offered to drop the indictments as part of a deal in which Noriega would give up power.

''I find very little incentive indicting foreign potentates if the State Department can negotiate them right out from under my feet,'' said U.S. Attorney Robert Merkle of Tampa. Merkle, who has indicated he'll quit if the indictment against Noriega is dropped, has refused comment on the reported investigation of Pindling.

Pindling has denied accusations of corruption and of taking bribes from drug smugglers.

The Miami Herald reported Monday that a grand jury in Orlando is hearing testimony against Pindling, the Bahamian leader since 1967. He was re-elected last year after his government was rocked by a drug corruption scandal.

The Herald, citing a ''well-placed source,'' said a July 4 deadline has been set for an indictment of Pindling.

But a federal law enforcement source, not identified further, said Justice Department officials who must approve such an indictment are likely to be reluctant because of the foreign policy problems caused by the Noriega indictments.

''You're going to have to have an awfully good case against a head of state before they're going to let anybody in the department do this again,'' the source said.

Another major obstacle, The Herald said, is statutes of limitations. The reported investigation of Pindling stemmed from testimony by prosecution witnesses in the federal trial of Colombian drug baron Carlos Lehder Rivas in Jacksonville. Lehder, prosecuted by Merkle, was convicted on all counts from an indictment that said he used the private Bahamian island of Norman's Cay as a cocaine transshipment point.

At one point in the trial, Merkle called Pindling ''a co-conspirator.'' Prosecution witness George Baron said he delivered a suitcase containing $400,000 to Pindling in 1980 for alleged protection of his pot-smuggling through the Bahamas.

But most of the allegations raised against Pindling in the Lehder trial involved incidents in the late 1970s and 1980, which would make them past the five-year statute of limitations.

Pindling denied Baron's story in particular and charges of corruption and bribe-taking in general in a May 4 statement. The Bahamian government ran full-page ads May 10 in The Herald, the New York Times and other newspapers stressing its commitment to fighting drugs and protesting the continued use of old allegations.

A 1984 Royal Commission of Inquiry detailed corruption in lower levels of the Bahamian government and law enforcement, but stopped short of linking Pindling to the drug corruption.

The Herald reported that U.S. drug-fighting officials say the Bahamian government has improved anti-drug efforts, participating in combined raids with the United States and allowing a U.S. Customs base on Gun Cay south of Bimini.

''We're at a very high level of cooperation at this point,'' said Customs spokesman Michael Sheehan in Miami.

''Operationally, the Bahamian government is cooperating very well,'' said Jack Hook, spokesman for the Drug Enforcement Administration.