The victims -- including a local police chief -- were rushed to hospitals with nails, nuts and bolts embedded in their bodies, said Yeni Rahmawati, a hospital spokeswoman.
Though houses of worship are commonly targeted by militants in Afghanistan, Pakistan and Iraq, the attack in the West Java town of Cirebon was a first for Indonesia.
Experts worry it could signal a "hardening" of local militants and a shift in tactics.
Indonesia, a secular nation of 237 million people, was thrust into the front lines in the battle against terrorism in 2002, when the al-Qaida-linked network Jemaah Islamiyah attacked two crowded nightclubs on Bali island, killing 202 people, most of them foreign tourists.
Several, less deadly suicide bombings have targeted Westerners since then. The most recent was two years ago, which experts attribute in part to a successful police crackdown.
In the last year, however, militants seeking to carve out an Islamic state have said the country's moderate leaders -- including the president -- and security forces would be their main targets.
They've since attacked several police posts, but never a mosque, and Friday's move showed just how little they seem to care now about public opinion.
Even former Jemaah Islamiyah members were outraged.
"To attack Muslims as their performing Friday prayers?!" said Abu Ghifari, who quit the group because he disagreed with some of its doctrines. "It's a great sin!"
The mosque stood on the grounds of a police compound, but was open to the public. Most of the wounded were officers.
West Java police chief, Maj. Gen. Suparni Parto, told El-Shinta radio the mangled body of the suicide bomber was found at the scene.
He was apparently wearing a suicide vest beneath his black Islamic robes and sitting among dozens of worshippers when he set off his bomb with a cry of "God is great!" said Agus Riyanto, a police spokesman.
Mardigu Wawiek Prasantyo, an intelligence analyst, called the attack very "worrisome."
He said it signaled a "hardening of militants," who have proved resilient despite a security crackdown that has yielded hundreds of arrests in recent years, with networks splintering and mutating.
President Susilo Bambang Yudhoyono, whose own life has been threatened in recent months, ordered an investigation.
"He's also called on the people, especially religious leaders, to help fight terrorists by reporting their whereabouts to authorities," Djoko Suyanto, a top security official, said.
Associated Press writer Niniek Karmini contributed to this report.