Peter Chapman, a local farmer, owns a £50,000 shareholding in agricultural co-operative Aberdeen and Northern Marts (ANM) Group.
It is seeking to expand of its operations at Thainstone, Inverurie, including a £4 million business park, and Mr Chapman called round Aberdeenshire councillors deciding on a forthcoming planning application, urging them to approve.
But he failed to mention his stake in the firm. He insisted it was an “honest mistake” and he did not stand to gain from its approval.
“It’s quite clear with hindsight that I should have made my financial interest in the phone calls clear and that it was a foolish oversight on my behalf not to do so,” he said.
“I failed to maintain the high standards of transparency that is expected of MSPs.
“As a result, I cannot in all conscience continue in post, hence my reason for offering my resignation.”
He added: “It was not my intention to hide this – indeed anyone can see the details of my investment on the Scottish Parliament register of interests.
“I can say hand on heart that my only thought was to support a local business and improve our local economy.”
Last year, Tory MSP Alexander Burnett was reprimanded and sanctioned by Holyrood’s standards committee for separate incidents where he failed to declare relevant interests.
Tory leader Ruth Davidson said she accepted Mr Chapman’s resignation from her front bench team “with regret”.
She told him: “I know your strong commitment in all things is to your constituents in the North-east, and that you will continue to serve them with vigour over the months and years ahead.”
But SNP MSP Stewart Stevenson urged Ms Davidson to “clean up her party.”
He said: “She really needs to get a grip of her self-interested colleagues on the Tory benches.
“The Tories think that they can do what they want and get away with it – but time and time again they get caught out. Peter Chapman is not the first, and I doubt he’ll be the last.”
Scottish Labour’s rural affairs spokesman Colin Smyth said: “Rather than holding the SNP to account, the Tories seem more concerned with intervening in local issues to further their own interests.
“The public deserve to know how this situation came about, who knew about it and when – and whether any other Tory MSPs have been engaging in similar behaviour on other issues. People in the North-east and across Scotland deserve answers.”