WASHINGTON — Federal and California regulators have begun an investigation into a second computer program in Volkswagen’s diesel cars that also affects the operation of the cars’ emission controls.

Volkswagen said that it had withdrawn 2016 models of its diesel cars from environmental certification in the United States because the company should have disclosed the software and sought regulators’ approval, but had not done so.

The disclosure of the software was made in testimony by the head of Volkswagen’s American unit, Michael Horn, before a House Energy and Commerce subcommittee hearing, and later confirmed by the Environmental Protection Agency and the California Air Resources Board.

The software qualifies under state and federal laws as a so-called auxiliary emissions control device — something that modifies the performance of emissions equipment. Volkswagen and regulators declined to say whether this software was intended to defeat emissions control tests, like the software that the automaker already admitted last month that it had installed in 11 million diesel cars since the 2009 model year.