The step follows a spitting attack on four officers inside a squad car by a drug addict with Hepatitis C. One female officer received infected saliva in her mouth as they struggled to subdue the detainee.
As well as being "humiliating and disgusting", the incident shows the real and present danger of infection while officers deal with violent cases, said Bremen interior ministry spokesperson Rose Gerdts-Schiffler.
Since September hoods have been issued to all police patrol vehicles in the northern city and were used on four occasions so far, she added.
There are on average one to four extreme cases of spitting at officers each month in Bremen, according to the spokesperson.
A heated debate ensued two years ago when Bremen Interior Minister Ulrich Mäurer first called for the introduction of such headwear, with opponents drawing comparisons with Guantanomo Bay-style detentions. But the official stands by their use.
"I regard the hoods as appropriate," Mäurer told the dpa news agency, stressing that they are only used once a person has started to spit or is already known to the police for spitting.
As well as saliva-borne infections, violent detainees often have mouth injuries and spit blood as well, raising the possibility of HIV infection, says the head of the Bremen police union, Jochen Kopelke.
"There are situations where attackers spit everything they have in their mouth," said Kopelke, rebuffing concerns that detainees are inhumanely incapacitated.
"You can see and hear in the hood," he said, referring to the thin mesh-like eye shield. Nor is breathing restricted, he added.
The head of Bremen's Left party, Kristina Vogt, said she understood why officers would want to protect themselves but found the hoods "problematic from a civil rights standpoint".
Sükrü Senkal, the interior affairs spokesman of the Bremen Social Democrats (SPD), also found the hoods to be "not optimal" in this respect and advocates a mouth mask only.
This is also not workable when dealing with thrashing detainees, objected Bremen interior spokesperson Gerdts-Schiffler: "Experience shows that a mouth covering quickly slips down."
The hoods will undergo a trial period of one year in Bremen before a decision is made on long-term use.
Other regions of Germany have also dabbled with the idea to a greater or lesser extent.
Schleswig-Holstein put the legal framework for their use in place in 2008 but has not issued them. Police in southern Bavaria occasionally use the hoods, while Lower Saxony did not allow them into service at all.