Former advocate Roseanna Cunningham, also Minister for Community Safety, repeatedly failed to disclose the shares in her parliamentary register of interests - which can be criminal offence punishable by a fine of up to £5000.
Cunningham, 63, last night insisted she had "no recollection" of the shares she has owned for 14 years, and said her office would take "immediate action" to inform Holyrood's authorities.
She also said she planned to sell the shares.
Labour said the matter now had to be fully investigated on a point of principle.
It is understood a member of the public last week lodged a complaint about Cunningham's non-declaration with the Commissioner for Ethical Standards in Public Life in Scotland.
Since 2000, when she helped create the company, Cunningham has owned 50 of the 750 issued shares in Left Review Scotland Ltd, the firm behind the Scottish Left Review magazine (SLR).
Cunningham and a group of fellow left-wingers, including ex-Labour treasurer Bob Thomson and Clydeside trade unionist Jimmy Reid, established the firm "to promote and reflect the principles and values of democratic socialism within the Scottish nation through the publishing of a magazine and organisation of discussion groups".
At the time, Cunningham was a deputy leader of the SNP, and was nicknamed Red Rose for her staunchly republican views.
Her firm still publishes SLR six times a year.
Since 2006, MSPs have been obliged to declare any shareholding in a company above 1%, but Cunningham has never declared her 6.7% stake.
Under the Interests of Members of the Scottish Parliament Act 2006, MSPs face exclusion from Holyrood for not declaring a "registrable financial interest" such as a shareholding.
This would require an investigation by the Commissioner for Ethical Standards in Public Life, then a recommendation from Holyrood's Standards Committee, and lastly a vote by MSPs.
Section 39 of the 1998 Scotland Act also states that any MSP who "takes part in any proceedings of the Parliament without having complied with, or in contravention of" the rules on declaring a registrable financial interest "is guilty of an offence" and "liable on summary conviction to a fine" of up to £5000.
It would be deeply embarrassing for any minister to have been found to have broken the law, but particularly for a justice minister. Cunningham's ministerial responsibilities include civil law.
On paper, her shares are worth £1 each. However, the latest company accounts valued the shareholders' funds at almost £10,000 at the end of 2012, suggesting Cunningham's original £50 stake is worth £650.
In a statement issued last night, the SNP said: "Ms Cunningham would like to take this opportunity to thank the Sunday Herald for drawing this to her attention - she has not been actively involved with or on the board of Scottish Left Review for several years and had no recollection of these shares having received no dividends or made any pecuniary advantage from them. Her office is now taking immediate and appropriate action to inform the relevant bodies at the Scottish Parliament.
"She is confident there is not -and has never been - any conflict of interests for any shareholding she has held and plans to divest herself of these shares."
Paul Martin, Labour's business manager at Holyrood, said: "The register of interests exists so the people of Scotland can have confidence in the integrity of those who represent them and that is why we have a responsibility to strictly adhere to it.
"If any MSP, not least the minister in charge of legal affairs, has failed to make a declaration, then this has to be investigated and dealt with on a point of principle.
"If we make exceptions in any case, then it opens the door to real abuse of our system and the bond of trust between elected politicians and the public will be further diminished."
A Scottish Parliament spokesman said: "We cannot comment on any individual member's Register of Interests; the onus remains on each member to register and declare financial interests in accordance with the Interests Act."