Unite said it had concerns that Ineos Group's arrangements "obfuscate the true position" of its activities.
Meanwhile, Ineos said the site, which it has shut down because of the dispute, would restart if Unite gave an assurance there would be no industrial action while the company consults workers over a survival plan.
The two sides are locked in a row which started over the treatment of a union convenor but now involves the future of the Scottish site.
The company has written to workers asking them to agree to changes to pensions and other terms and conditions as part of its survival plan to prevent the site's closure.
Unite said the move amounted to an ultimatum for workers to agree to worse pay and conditions by 6pm on Monday or face the sack.
Scotland's First Minister Alex Salmond held separate talks with the two sides in an effort to break the deadlock, which has led to the site being shut down.
Ineos said it would restart the Grangemouth site if the company received a guarantee that there will be no further industrial action of any kind during the 60-day consultation period.
Calum Maclean, Grangemouth chairman, said: "We have been very clear that for compelling safety reasons, we cannot restart the site until we know that the risk of further industrial action has been removed."
Writing to Chris Davidson, head of the anti-avoidance group for the HMRC, Unite general secretary Len McCluskey said: "The current uncertainty as to the true nature of the company's UK activities is causing genuine confusion, not least to the Ineos employees we represent, as well as other stakeholders.
"Analysis of the company's accounts is in itself made difficult by the sheer number of reorganisations undertaken by the Ineos Group. However, analysis of the latest 'Chemicals' accounts (2012) shows a fundamental paradox worthy of investigation at the heart of the company's accounting position.
"My union has employed expert external analysis for the purpose of trying to better understand Ineos at a time of great uncertainty. On the back of our findings I now urge the HMRC to launch a formal investigation into the affairs of Ineos."