One-third of the 21 MX nuclear missiles cannot be fired for lack of guidance systems, the Air Force acknowledged yesterday as three civilian whistle-blowers warned Congress that the remaining MXs could not hit their targets because of shoddy workmanship.

The delays in reaching operational status for the 21 MXs in Minuteman silos, together with the assertions made before the House Armed Services Committee yesterday, have generated new doubts in Congress about the blockbuster weapon that President Reagan has championed.

An Air Force spokesman said the guidance systems missing from the seven missiles are being used for testing and training and could be put on line if necessary. He added that 17 successful test flights of the MX have demonstrated the missile's reliability.

"If the national-security situation dictated," Brig. Gen. Edward P. Barry Jr., commander of the Air Force Ballistic Missile Office, said last night, "we have sufficient guidance systems to field all 21 missiles." He added that the reliability of the 14 on alert is 20 to 50 percent better than previously expected.

But House Armed Services Committee Chairman Les Aspin (D-Wis.) said he is not completely satisfied with the MX program after hearing yesterday's witnesses. He said the seven MXs failed to become operational on schedule because Northrop Corp. did not deliver guidance systems on time. The Air Force considers the delay serious enough to hold back $72 million in payments to Northrop.

Aspin also said Northrop apparently took "short cuts" in manufacturing and testing to get guidance units delivered to the 14 missiles that the Air Force certified as ready to fire. "Now the real question is, what confidence can we have in the 14 MX missiles that are out there?" Aspin said. "We're not sure they meet the standards."

He and several other lawmakers complained that the Air Force had repeated a tactic on the MX that it used on the B1 bomber -- waiting until the last moment to inform Congress about technical problems. Aspin said the committee did not learn the scope of the B1 problems until the defense budget was submitted in January and was kept in the dark about MX difficulties until March.

"It's going to lead to more micromanagement of the military by Congress," said an angry Armed Services member John G. Rowland (R-Conn.), a staunch MX supporter. He said he will introduce legislation requiring the military to notify Congress as soon as a weapon encounters major technical problems.

"When you support a program of this significance," Rowland said, "and there are allegations like this floating around" about technical problems, "and the Air Force isn't notifying you until the horse is already out of the barn, we're going to make sure the horse stays in the barn until we know what's going on."

David Peterson and Bryan Hyatt, former employes of Northrop's Electronics Division, which makes the MX guidance system, and Jeffrey Kroll, a current employe there, testified to shoddy work and questionable accounting practices as they sat side-by-side at the committee witness table yesterday.

"Northrop's procurement system became so backlogged that parts were actually being bought with cash by workers and put into hardware without being inspected or tested at all," Peterson said, an engineer at the electronics division from 1982 until this year when he said he was fired for challenging company practices.

The MX guidance system is called IMU, for inertial measurement unit, and Hyatt, a former microelectronics engineer for Northrop, criticized what he called faulty bonding and lack of testing of the miniature parts within the IMU.

"Many, if not all, of the IMUs presently being used in the missiles located at Francis E. Warren Air Force Base {near Cheyenne, Wyo., where MX missiles are deployed} will fail upon launch," Hyatt said.

Northrop's procurement became so disorganized at one point that a mountain of extra parts piled up at the electronics plant, Kroll said. To keep government inspectors from discovering the surplus, he said, company officials ordered thousands of parts the government had paid for to be thrown out, filling up a dumpster 24 feet long and 12 feet wide.

"There is something very, very wrong with the present system that we operated under," he told the committee.

John Thorne, a Northrop spokesman, said the testimony consisted of unproven allegations. He added that Northrop has installed a new management team at the California electronics division to address problems there.