The statement said that this type of blood clot needed a different treatment than usual.
The common treatment – an anticoagulant drug called heparin – “may be dangerous”, it said.
Pending a further review, the FDA and CDC recommended “a pause in the use of this vaccine out of an abundance of caution”.
This was to “ensure that the health care provider community is aware of the potential for these adverse events”.
All six cases were in women aged between 18 and 48, with symptoms appearing six to 13 days after vaccination.
One patient died from blood clotting complications, while another is in a critical condition, the FDA’s Peter Marks confirmed.
The joint statement said that “people who have received the J&J vaccine who develop severe headache, abdominal pain, leg pain, or shortness of breath within three weeks after vaccination should contact their health care provider”.
The federal government is now likely to pause the use of the vaccine in all federally run vaccination sites, and to expect state sites to do the same.