In an interview, Mr. Mahaney said stock-based compensation could “distort the quality” of a company’s earnings and “make them look stronger than they are.”

Mr. Mahaney has identified Twitter, LinkedIn, Yahoo and Alibaba as among the tech companies that are highly dependent on stock to pay their employees. In a report, he wrote that Twitter’s stock-based compensation over the last two years accounted for 39 percent of the company’s revenue, on average, the highest percentage of any Internet company.

LinkedIn, whose share price is down about 48 percent this year, did not respond to requests for comment. Twitter, whose stock is down more than 20 percent this year, also did not respond to a request for comment.

Another tech company that Wall Street analysts are examining for its stock-based compensation expenses is Workday, which sells human resources and financial management software. The company is expected to increase its stock compensation about 48 percent in its 2017 fiscal year, which is faster than its revenue is projected to grow, according to Sarah Hindlian, an analyst at Macquarie Group.

In an illustration of how stock-based compensation expenses can affect a company’s results, Ms. Hindlian says Workday’s margins are projected to be around negative 25 percent for fiscal year 2017. But when the company’s $370 million in stock-based compensation is excluded from results, its operating margins are much better, coming in around zero.

Workday’s heavy reliance on stock-based compensation has been a factor in Ms. Hindlian’s projections for the company’s share price. Last month, she forecast that Workday’s stock would trade at $49, down from its current price of about $77. She has a sell recommendation on the stock.

Ms. Hindlian says that while it can be reasonable for companies to pay workers a lot in stock, the practice can become scary when the stock starts to fall. “Particularly with software companies, you run the risk of losing your leading salespeople, engineers and developers when the stock falls, because employees feel like they’re getting a pay cut,” said Ms. Hindlian, who also rang the alarm on LinkedIn’s use of stock-based compensation over a year ago.