Bernie Madoff didn’t just generate phony profits. He paid phantom employees, the federal government says.

The payroll of Bernard Madoff Investment Securities LLC “included many individuals — friends and family of BMIS insiders — who did not perform any work for the firm, but who nevertheless received salaries and benefits,” the Securities and Exchange Commission said Monday.

The allegation was contained in documents charging Eric Lipkin, a former Madoff employee, with helping Madoff perpetrate his epic Ponzi scheme.

Lipkin, 37, pleaded guilty Monday to criminal charges including conspiracy, falsifying books and records, and bank fraud, the Justice Department said.

He also settled civil fraud charges with the SEC, agreeing to give up ill-gotten gains and pay a fine to be determined by a court.

Lipkin agreed to cooperate with the government, which is still trying to determine whether anyone else was involved in Madoff’s fraud and where all the money went.

He had worked for Madoff’s firm since he was a teenager performing clerical tasks for his father, who was the company’s controller for many years, the SEC said. He was still employed there when Madoff’s scheme collapsed in late 2008, costing investors billions of dollars, the government said.

Lipkin received annual bonuses that were in part a reward for helping to mislead auditors and examiners, the SEC said. Madoff gave Lipkin $720,000 to buy a house, and by 2008 he was receiving an annual salary of $225,000, the SEC said.

Lipkin created false payroll documents for “no show” employees, the government said. He pleaded guilty to, among the other charges, reporting false information about pensions and benefits to the Labor Department.

Lipkin also helped generate documents related to the Ponzi scheme, including bogus trading records behind phony balances shown on clients’ account statements, the government said. The aim was to deliver “the rate of return promised to the account holders by Madoff,” the Justice Department charged.

Several other Madoff associates have been charged in connection with the fraud. One of them, Frank DiPascali, has pleaded guilty.