Solyndra LLC, a California solar-panel maker once hailed by President Barack Obama as "the future" of clean energy, is the target of a criminal investigation into whether its executives knowingly misled the government to secure more than $500 million in loan guarantees, said people familiar with the matter.

Agents from the Federal Bureau of Investigation on Thursday raided the company's headquarters in Fremont, Calif., carting away documents and computer equipment as part of the previously undisclosed federal probe.

The...