The chairman of Ineos, the oil refinery firm in Grangemouth that employs Unite's Scottish chairman, Stevie Deans, said the discovery was made during an investigation into the shop steward.
However, Unite members at the plant have voted for strike action over what the union describes as the "victimisation" of Deans.
Unite, which is Labour's biggest union affiliate, has been under pressure over its tactics in allegedly trying to secure the party candidacy in Falkirk for Karie Murphy.
The union signed up around 100 new members, some of whom are believed to be linked to the Ineos plant, a recruitment surge that triggered an internal Labour inquiry.
Murphy and Deans - who is also chairman of the local Labour party in Falkirk - were suspended by the main Labour Party, but cleared after key evidence was withdrawn during the inquiry.
Ineos launched its own investigation into Deans, a longstanding employee, which is believed to focus on whether company resources were used for the purposes of the Labour selection.
In a letter to staff last week, Ineos chairman Calum MacLean stated: "The investigation of Mr Deans on a limited search of his emails has revealed over 1000 emails associated with the Falkirk West election. The company has therefore decided to carry out a fuller search.
"This search will be carried out by a third party and will be complete by 18th October. Ineos management will decide whether action needs to be taken by 25th October."
However, Unite says Deans was initially cleared and reinstated by the firm, and accuses the company of singling out its official.
After balloting its members earlier this month, Unite announced on Friday that 81.4% of those who voted backed strike action.
A shut-down could result in the vital oil refinery effectively being closed due to a row over issues relating to a Labour selection contest.
In a sign of the tensions between the union and the employer, Ineos is taking legal action against Unite about a statement on the union's website it says is libellous.
Unite officials have also urged Finance Secretary John Swinney at a recent meeting to intervene.
MacLean said: "We will not be intimidated by union pressure. We cannot have one rule for union officials and another for everyone else on the site.
"I would urge union members to reflect on what they have been told by the union and think carefully about how they vote on this issue."
It is understood employees have gone through the Ineos disciplinary process in the past, without the action triggering a strike ballot.
A Unite spokesman said: "Stephen Deans was cleared and then reinstated. Unite is deeply concerned that, irrespective of these facts, Ineos, which is majority-owned by Jim Ratcliffe, is continuing with a campaign of unfair treatment against an innocent employee."
A Scottish Government spokesperson said: "The Scottish Government has been in discussion with both Unite and Ineos management.
"We are disappointed that discussions to date have yet to resolve the issues between the two sides and we urge the union and Ineos managers to work together to achieve a settlement.
"We will continue to offer any support that would facilitate those talks."