BNFL said that it had made a series of formal complaints about 'apparent violations' of the prohibited airspace around Chapelcross nuclear plant in Dumfries and Galloway, by military and civil aircraft.
Reports of nine alleged breaches involving 15 aircraft had been compiled from eyewitness accounts over the past four years.
A civil pilot was recently prosecuted for breaching the zone. BNFL said: 'It is known that there is a military flight-path in the area, but an assessment has shown that the probability of an aircraft crashing into the site is very low indeed.'
This followed remarks made by Alan Dutch, a senior safety assessor at Chapelcross, during a public meeting about low flying, in the nearby town of Annan on Tuesday night.
Because of the risk of an accident, aircraft are prevented from flying under 2,400ft within a two- mile radius of nuclear plants.
Robert Robinson, a local farmer, said the rule was broken four and a half weeks ago. 'I was busy in a field and four or five jets came over, certainly no higher than 500 feet, less than two miles from Chapelcross,' he said.
RAF Wing Commander Geoff Coop told the meeting that he was 'amazed' by the allegations. He promised a full investigation and disciplinary action against any pilot found guilty of violating the zone without good reason.
The Ministry of Defence said last night that since 1989 it had received five complaints from BNFL about low flying. In three cases there had been no infringement of Chapelcross's air space, and two complaints made earlier this year were still under investigation.
An MoD spokesman said that pilots were requested to avoid the air space around nuclear plants but it was not mandatory. Between January 1991 and April 1992 there had been 173,470 low-flying training sorties in the UK.
Chapelcross, commissioned in 1958, is Britain's second oldest nuclear station, which - as well as producing electricity - supplies the MoD with plutonium and tritium for use in nuclear weapons. It is just 10 miles from Lockerbie, where a PanAm jumbo jet crashed in December 1988.
Anti-nuclear campaigners say that the consequences of a jet hitting a nuclear power station would be catastrophic.
Mike Townsley, from the Scottish Campaign to Resist the Atomic Menace, said: 'If the jet hit the right place and caused a breach you could have a massive release of radiation, laying waste to large parts of southern Scotland and northern England.'
He added: 'Hearing BNFL criticise other people for lack of safety is extraordinarily ironic. The whole issue of low flying and nuclear stations should be urgently reviewed - especially in the light of recent events.'
In evidence to the 1988 inquiry into Hinkley Point C in Somerset, the electricity industry accepted that if a military aircraft weighing more than 2.3 tonnes crashed into a nuclear reactor, there would be a 15 per cent risk of an uncontrolled release of radiation.