Geoconsult claimed that the prosecution 'behaved in a grossly unfair way which led to two serious criticisms of the Health & Safety Executive by Mr Justice Cresswell' in a statement issued on Tuesday.
It confirmed that it had instructed its lawyers to lodge an appeal against its conviction and fine.
It said: 'The first (criticism) was that Mr Martin Thurgood, a principal inspector of the HSE, wrote or substantially influenced no fewer than 81 of the 120 pages of the prosecution's main expert witness Mr Guy Lance, the Director of Tunnelling of WS Atkins.'
HSE withdrew the Lance report shortly before the jury was sworn in, after the defence had claimed the report was influenced by Thurgood.
HSE barrister Hugh Carlisle QC denied that there had been any deliberate attempt to direct Lance's opinions and said there was no intention to turn him
into a prosecution advocate. He also argued that there had been a misunderstanding of the rules on the use of expert witnesses.
Originally the HSE had brought charges against Geoconsult and Balfour Beatty over similar NATM work at Heathrow Terminal 4, although these were later dropped.
'There is a strong suspicion that bringing the charges in respect of Terminal 4 was little more than a cynical ploy to force Balfour Beatty to bargain with the prosecution to drop the charges relating to Terminal 4 in exchange for pleas of guilty in respect of the charges,' says the Geoconsult statement.
The statement also points to the fact that prosecution expert witness Sir Alan Muir Wood gave evidence to the effect that it was morally wrong for Geoconsult 'to be prosecuted when others (in his view culpable) were not there'.
An HSE spokesman said it was inappropriate for the prosecution to comment on the actions of a defendent. 'The defendant has a legal right to appeal,' he said.