The Reagan administration's war on drugs is troubled by delayed equipment, financial woes and - in a new twist - a corporate giant withholding use of a herbicide for spraying South American coca crops.

Complaints about these and other frustrations with the drug war were lodged with a House Government Operations subcommittee Wednesday by the very agencies waging the fight. The hearing was to continue Thursday.The Coast Guard said its boats and planes often sit idle because the agency is short of money.

The Customs Service admitted the entire Southwest border with Mexico remains a haven for airborne drug smugglers because of delays in installing four of five radar balloons.

The State Department said it couldn't understand why Eli Lilly & Co. would refuse to allow use of a "safe and effective herbicide" to destroy the crops used in making cocaine.

And that's not all.

Coast Guard surveillance planes have cracks in their wings and may be grounded this summer. New or modified planes authorized by Congress have not yet been delivered. Construction of three new command, control, communications and intelligence centers for the drug war are behind schedule.

Rep. Glenn English, D-Okla., chairman of the subcommittee, blamed the Customs Service for the delays in installing radar balloons along the porous Southwest border to detect airborne drug smugglers. Only one of the five balloons, called aerostats, is in operation.

"This is a terrible failure," he told William Rosenblatt, Customs Service enforcement chief. "You are costing us dearly. There's no sense of urgency about this. That's the problem."

The latest roadblock in the drug fight was described to the committee by an incensed Ann B. Wrobleski, assistant secretary of state for international narcotics matters.

She said the Lilly company has decided to withhold the herbicide tebuthiuron, known as "spike," even though it has been manufactured for more than 15 years, has been proven safe by U.S. standards, is widely available in this country and has been sold to the Interior Department.

English said he was "stunned and outraged" at Lilly, called the company "a deserter" in the drug war, and invited company officials to testify on its position.

The company reiterated a statement it made last month saying "a number of practical and policy considerations preclude our participation in this specific program."

Meanwhile, at the State Department, spokeswoman Phyllis Oakley said, "We think the short-term impact is serious." The department wanted to test the chemical for use in eradicating the coca crop focused mainly in Peru's Huallaga Valley, she said.

At the hearing, Coast Guard Commandant Paul A. Yost said his new, fast patrol boats and many of the agency's airplaines are operating at only 55 percent of last year's levels due to lack of money.

He testified it was ironic that Congress is ready to spend huges sums for an escalation of the military's role in the drug war, but can't find $60 million to get his vessels in the water and planes in the air full time.

"Turn me loose and don't give my mission away," he told the committee.

Rosenblatt blamed the radar baloon delays on problems with site selection, environmental concerns, competitive bidding, and bureaucratic roadblocks from other federal agencies.