Stephen Deans, who quit his job at the plant yesterday, is alleged to have held the personal details of local Labour members on his Ineos computer during an internal party selection contest.
Members are understood to have been given a ranking laying out their political sympathies - three stars meant they were politically sympathetic to Unite's aims, while one star indicated a lack of support.
The Information Commissioner has said it is looking into the circumstances of the alleged breaches before deciding whether to take further action.
Mr Deans is chairman of Unite in Scotland and of the Falkirk West Labour Party. He is at the centre of claims he made "inappropriate use of company resources and systems" - using company time and equipment for the union's political work.
Operators Ineos threatened to close the petrochemicals side of the Grangemouth plant last week in a bitter dispute with the union, which represents many of the 1350 workers, over terms and conditions.
The closure would have resulted in 800 job losses and threatened the oil refinery on the same site.
The conflict was initially sparked by Unite backing a strike over Ineos pushing ahead with a separate investigation into Mr Deans, which would have culminated today.
The Swiss-based company launched a probe into whether Mr Deans had used company resources to work on Labour's selection of a Westminster candidate for Falkirk.
Unite had strongly supported left-winger Karie Murphy for the candidacy and Mr Deans helped recruit a raft of new members in the constituency, some of whom worked for Ineos.
The circumstances of the mass sign-up led to Mr Deans and Ms Murphy being suspended by Labour, only to be reinstated after key evidence was withdrawn by witnesses. However, Ineos pushed ahead with its own investigation, which ended last week.
Yesterday, 24 hours before Ineos was due to reveal the outcome of the case, Mr Deans quit his job at the company.
Hundreds of emails relating to the Labour selection are believed to have been found on his computer, some of which Ineos passed to the police following legal advice.
An Ineos spokesman said: "The company has conducted a thorough investigation into Mr Deans's activities over the last 18 months and made Mr Deans aware of these findings last week. Mr Deans requested an additional five days prior to the final disciplinary hearing to allow him time to provide any further relevant information. The company was due to meet with Mr Deans again tomorrow but has now received his resignation."
Company lawyers uncovered emails said to include a draft of the retraction letter which was sent to Mr Deans for him to get it signed by Michael and Lorraine Kane, the witnesses who initially complained to the party against him and Ms Murphy.
Mr Deans has told the Unite members in the plant it was "entering a new period, and my own situation would only prove to be a distraction, and would cast a shadow over what we all must hope will be a prosperous long-term future for the plant."
He told Ineos in his resignation letter that management now treated him as the "enemy within".
At Westminster, Tories demanded that Ed Miliband reopen Labour's Falkirk selection inquiry. Conservative chairman Grant Shapps said: "Stevie Deans's resignation is yet another reason why Ed Miliband must finally act. He must publish the internal Labour inquiry into Falkirk.
"Ed Miliband should also open a new inquiry to investigate properly the initial allegations of selection rigging and Unite's attempt to subvert the internal inquiry. If he backs down to Len McCluskey yet again, how can he possibly stand up for hard-working people?"
Labour backbencher Jim Sheridan, who chairs Unite-sponsored MPs, said Mr Deans's resignation was unfortunate given he had worked at Grangemouth for 24 years.
He said: "He has been caught up in a political storm. Stevie did something wrong and has paid the ultimate price and lost his job and his livelihood. But hands up all those who have used business emails for private messages.
"The thing that worries me is the people who have advised Ed Miliband; they need to be accountable to the membership of the party. Ed has been ill-advised throughout. There are a number of people who need to take responsibility."
He dismissed Conservative calls for Mr Miliband to reopen the party's inquiry into Falkirk as political grandstanding. He instead suggested the inquiry they should be demanding was one into the tax affairs of Swiss-based Ineos owner Jim Ratcliffe.
A spokesperson for the Information Commissioner's Office said: "We have recently been made aware of a possible data breach. We will be making enquiries into the circumstances of the alleged breach of the Data Protection Act before deciding what action, if any, needs to be taken."