Veeco Instruments Inc. is challenging recommendations by two major proxy advisory services that its shareholders vote against the company's executive compensation plan.

Plainview-based Veeco, whose equipment is used to make light-emitting diodes, or LEDs, organic LEDs (OLEDs) and computer hard drives, issued a Securities and Exchange Commission filing on Thursday that seeks to rebut reports by Institutional Shareholder Services (ISS) and Glass, Lewis & Co., which counsel institutional investors on proxy issues.

"Veeco respectfully disagrees with the analysis and recommendations of the advisers," the company said. Veeco officials declined to comment beyond its filing.

Josh Henke, managing director of Longnecker & Associates, a corporate governance and compensation consultancy in Houston, said that government reforms put in place after the financial crisis of 2007-2010, allowing nonbinding "say-on-pay" votes on executive compensation, have prompted increasing friction between companies and proxy advisory firms.

"This has been an ongoing battle for the previous few years," he said. "You'll see companies filing additional disclosures to push back."

Veeco disagreed with the proxy advisers on issues including the proper benchmarks for measuring the company's total return to shareholders, and even the amount of money that Veeco executives are being paid.

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For instance, ISS analysts concluded that Veeco CEO John Peeler received compensation worth $3.3 million in 2013, versus the median CEO pay of $2.5 million in a group of peer companies.

Veeco, however, put Peeler's total compensation at $2.9 million. The disagreement largely stems from different methods of calculating a current value for stock options that can be exercised in the future.

Manhattan-based consultancy Towers Watson reported that 2 percent of U.S. companies failed their say-on-pay votes in 2014, but as of March 10, shareholders had rejected the proposal of only one Russell 3000 company.

Henke said that companies have been privately jawboning major shareholders to avoid an embarrassing loss on the vote.

Veeco's largest shareholders as of March 14 were four investment firms: BlackRock Inc. with 16.5 percent of outstanding shares; Joho Capital LLC, 6.3 percent; Eagle Asset Management Inc., 6.3 percent, and Vanguard Group, 6.2 percent.

The company's annual meeting will be held in Plainview on May 6.