The admission by Vattenfall Europe came after police searched offices at the site of the reactor at Krümmel, near Geesthacht, 30 kilometres south-east of Hamburg.
In a report on the incident to regulators that was available on the company website Saturday, Vattenfall said there was a breakdown in communications between the reactor operator and the shift manager.
The misunderstanding involved the operation of valves designed to slow a rise in pressure in the reactor's casing, following the failure of a water pump, the company said.
The operator opened two valves for several minutes, instead of alternately opening and closing them as the manager wanted. As a result, pressure dropped rapidly in a short period, Vattenfall said.
The Swedish company has been forced to defend itself over its public handling of the June 28 incident, which led to the reactor being shut down.
Police searched offices at the nuclear plant Friday as part of an inquiry into a possible offence during the fire at the site, state prosecutors said.
The legislature of Schleswig-Holstein state warned the Swedish-owned company Vattenfall Europe that it might lose its license to operate Krümmel power station east of Hamburg. It called on company officials to testify at a state parliamentary inquiry next week.
Prosecutors in the city of Lübeck said detectives were sent to the site to inquire into reports that a reactor operator had to wear a face-mask when smoke from burning oil entered the control room during last month's fire.
It was possible the man had been harmed by toxic fumes and that the company might have caused bodily harm by negligence, spokesman Klaus-Dieter Schultz said.
Representatives of the Swedish company, however, told police officers that this was not the case.
"The safety of our staff is a top priority for us," Bruno Thomauske, the chief of Vattenfall Europe Nuclear Energy, said in a statement.
Vattenfall had declined to name the operator so that he could be interviewed. The detectives sought the name in records in the control room and offices at Krümmel.
The company denied obstructing the inquiry and said it had vainly tried to contact prosecutors on Thursday.
"We are cooperating fully with the authorities and the state prosecution and are doing everything to clear up this matter," Thomauske claimed. "We have explained that nobody was injured."
Gitta Trauernicht, the state's minister responsible for reactor safety, said in the Schleswig-Holstein parliament on Friday she would use all her powers to force improvements at Krümmel, one of 17 nuclear power stations in Germany.
"I've used the full range of legal means and ensured that Krümmel remains deactivated," she said.
She said she would insist it be in perfect order before it resumes operations, and added that she would not be deterred by demands for compensation from the company.
She said the day of blunders at Vattenfall had been "unique" in the history of the German nuclear industry.
Two Vattenfall nuclear stations in the state failed on June 28, one because of a short-circuit and the one at Krümmel when its transformer caught fire. Neither reactor was damaged. The fire at Krümmel broke out just hours after the nuclear reactor at nearby Brunsbüttel had to be shut down temporarily because its capacity was overloaded.
The company initially said the fire at the Krümmel plant had been isolated from the atomic reactor but, according to the regional social affairs ministry, the flames had reached the building housing the reactor.
The ministry also contends that Vattenfall waited five days to report technical problems that occurred when workers tried to restart the Brunsbüttel plant.
Vattenfall has since admitted further mechanical mishaps including the smoke entering the control room.
German anti-nuclear groups have demanded that the company's nuclear license be revoked. Under current legislation, all Germany's nuclear power plants are to close by 2021.