Mr Pereira will return to the Hutt Valley cigarette factory he had worked at for 35 years, most recently as the material stores supervisor.
He was fired over serious allegations about his behaviour on three specific occasions between February 2010 and last March and other unspecified occasions.
Complaints about specific incidents were made by three people who reported to him and his manager.
According to the authority, Mr Pereira was accused of being "aggressive and intimidating" and "creating an unsafe and fearful working environment".
His manager, Graham Chote, said Mr Pereira had "verbally and physically" threatened him and behaved in an "insubordinate manner".
At a disciplinary meeting, he was accused of scaring one team member into hiding when he was "in a mood".
Another said Mr Pereira made him "afraid to go into the office" and "blew up" when it was suggested things could be done differently.
In addition, other employees described a "fearful and intimidating workplace as created by [his] behaviour", said the ruling.
Mr Pereira was suspended on March 18, attended a disciplinary hearing on March 31 and mediation in April. He was fired by factory manager Mike McInnarney after another meeting on April 12, at which he apologised for his behaviour and said he would change.
The authority found five reasons Imperial Tobacco's inquiry was flawed.
They included that it addressed incidents that could have been dealt with earlier and that the allegation about a "fearful working environment" lacked sufficient detail for Mr Pereira to be able to respond fairly.
It also noted that Imperial's human resources department had not been consulted about the process.
The authority ordered Imperial to reinstate Mr Pereira within 28 days of the ruling, made on January 25.
It said it was satisfied there were "reasonable prospects" he could return to being a "harmonious and effective" team member.
Mr Pereira's lawyer, Carolyn Heaton, said he was looking forward to going back.
Imperial Tobacco said it might appeal.
