When five workers at Stavis Seafoods in South Boston smelled ammonia at the end of their shift Wednesday, they pushed an emergency switch to shut off a valve, then rushed out the door.

But the outpouring of ammonia didn’t stop, fire officials said. Only four of them made it out of the building alive.

“The valve should have shut off by hitting the switch,’’ said Steve MacDonald, a spokesman for the Boston Fire Department, one of several agencies investigating the fatal leak.

The ammonia leak was found in a ruptured 1½-inch metal pipe on the second floor of the cold storage warehouse, MacDonald said Thursday. It is not clear what caused the pipe to break, he said.

Authorities and the company have not identified the worker who was overcome by ammonia fumes Wednesday, a fatality now under investigation by the federal Occupational Health and Safety Administration. The man was found in a second-floor stairwell by a fire department hazmat crew.

The fatal leak recalled previous concerns there raised by federal regulators, although violations related to the handling of ammonia were later dropped. In 2009, OSHA cited Stavis Seafoods for 15 serious violations of workplace safety rules, including the company’s safety program for handling of “anhydrous ammonia’’ in the facility’s refrigeration system.

OSHA inspectors later determined that because the plant used less than 10,000 pounds of ammonia, it was not required to comply with that safety program, according to OSHA spokesman Edmund Fitzgerald.

OSHA withdrew the nine citations related to ammonia, he said. The remaining infractions involved hazardous waste operation and emergency response, respiratory protection, control of hazardous energy, medical services and first aid, and powered industrial trucks, OSHA records show.

“None of them were related to ammonia,’’ Fitzgerald said.

Stavis was initially fined $47,250, but after the nine citations were withdrawn, the fine was reduced to $15,750,records show.

The case was closed after the company paid the fine, he said.

Fitzgerald said it is far too soon to identify what caused the leak, and that the investigation will likely take weeks or months.

In a statement released Thursday, Stavis Seafoods chief executive Richard Stavis said the company will cooperate with investigators.

“Our concern today is with the tragic death of our employee, his family, and finding out exactly what happened,’’ Stavis wrote. “The safety of our employees and our workplace is always our greatest priority. To that end, we will do everything we can to assist with the investigation.’’

On the South Boston waterfront, news of the worker’s death spread quickly. The owner of Pete’s Dockside, a nearby breakfast-lunch spot, said many Stavis workers are regular customers.

“They’re a tight-knit group,’’ Tony Barros said, standing behind the counter at lunchtime. “They all get along well.’’

On Thursday, the Stavis workers who ate there “seemed heartbroken,’’ Barros said, as did workers from other fish processing plants.

“It’s all hard-working people down here who work in the fish plants, trucking companies,’’ he said. “It’s very upsetting.’’

Barros said he believed the worker who died was a regular customer who many days ate breakfast and lunch there. On Wednesday, the man came in at a little after 1 p.m. and ordered a cheeseburger with light barbecue sauce and french fries, Barros said.

“I waited on him,’’ he said. “Because of that, I noticed him a little more.’’

“Tony,’’ he said, nodding toward a cook standing at the grill to his right. “He cooked him his last meal.’’

Firefighters rushed to the warehouse at 6 p.m. Wednesday. The four workers who made it out safely told them that one worker was still inside, MacDonald said.

The firefighters tried to rescue him but were unsuccessful.

“They tried to get up the stairs to where he was,’’ MacDonald said. “They had air tanks, but not protective suits. The sheer volume of ammonia pushed them back.’’

Members of the hazmat unit entered the building wearing full protection suits, but could not reach him in time.

The shut-off valve for the ammonia was in the middle of the building on the second floor, slowing the emergency response, MacDonald said.

“Usually [the shut-off valve] is located near the entrance. That’s also something we will be looking at as far as the cause,’’ he said.

The valve was finally closed after 9 p.m., officials said.

“Once [an accident] becomes a recovery operation and not a rescue, everything is slowed down,’’ MacDonald said. “Everything is done in a safe manner, especially when you are dealing with hazards such as ammonia.’’

Kathy McCabe can be reached at Katherine.McCabe @globe.com. Follow her on Twitter @GlobeKMcCabeJohn R. Ellement can be reached at ellement@globe.com. Follow him on Twitter @JREbosglobe.