The guideline to the sellers was made by the government at its session at which it reviewed a report from the Slovenia Sovereign Holding (SSH) on Agrokor's takeover of Mercator.
It asked the sellers "to lead all procedures with due care and diligence and to consider in their decision aspects of employment, relations in the food chain and other factors important to the Slovenian economy".
However, the government failed to go as far as take a final recommendation for or against the sale, instead requesting more information from the SSH.
The SSH, which manages state business interests, was also tasked with monitoring the sale process and keeping the government abreast with the latest developments.
The sale of Mercator to Agrokor has become a hot political topic ahead of the 13 July general election, with at least two parties in the outgoing government making a stand against the sale.
The leaders of the Social Democrats (SD) and Pensioners' Party (DeSUS), Dejan Židan and Karl Erjavec, have been outspoken in opposing the sale.
"It is clear that Agrokor lacks the backing of serious capital while there is also data which shows that the sale of Mercator would big a major blow to…Slovenia's food industry," said Erjavec ahead of the cabinet session.
The trade unions have also demanded government action to stop the sale.
The opponents of the sale fear that Agrokor, which is major producer of food in Croatia, will replace Slovenian products with its own on Mercator's shelves.
They also argue that Agrokor is unfit to own Mercator, which has struggled to manage nearly EUR 1bn in debt, because of its own indebtedness.
But it remains unclear whether this is the prevailing view in the government, as no direct decision has been taken on whether to support or oppose the takeover to date.
Indeed, speculation about a rift in the cabinet ranks have swirled since last week, when it first debated the takeover.
The government's influence over the sale stems from the state-controlled members of the consortium of sellers, including the NLB and NKBM banks and the Pivovarna Laško beverage group.
The SSH, which was established less than ten days ago, has appeared tentative in trying to force the issue given that procedures for the sale in the final stages.
Agrokor and the sellers set the end of June as the deadline for the transaction.
Unofficial reports from before the cabinet session suggested the SSH had not drawn up a report demanded by the government.
Its chairman Matej Pirc later denied this by saying that the holding reported to the ministers in oral form as well as in written form to the government.
However, it subsequently emerged that the state-owned banks involved may have been stingy with the information provided to the SSH.
Well-placed sources said that while NKBM provided some information, NLB failed to reply to the SSH request.
The current offer of EUR 86 per share plus a EUR 225m recapitalisation, valid until 30 June, would see Agrokor pay over EUR 400m for the 53% stake in Mercator.
Of the EUR 225m capital injection, EUR 200m would go to creditor banks and the rest for working capital; the creditor banks are to chip in EUR 100m in loans.
Mercator recently reached a financial restructuring deal with creditor banks and leasing institutions on extensive financial restructuring which would allow it to implement its strategy for turning around operations independently.