The 32-year-old dead officer was part of a special forces unit dispatched to the scene to enforce the order.
A German police officer died on Thursday of gunshot injuries sustained in a raid against a member of the shadowy far-right group "Citizens of the Reich", authorities said.
Police in the southern state of Bavaria said "the critically injured officer died in the early morning hours in hospital" after the standoff on Wednesday.
The 49-year-old gunman belonging to the so-called Reichsbuerger movement, identified only as Wolfgang P., was also slightly injured in the struggle with officers in the town of Georgensmuend and taken into custody.
Local authorities had ordered the seizure of the man's arsenal of about 30 firearms after his permits were rescinded due to a determination that he was psychologically "unsound".
The 32-year-old dead officer was part of a special forces unit dispatched to the scene to enforce the order. Three other officers were injured in the confrontation, one of them seriously.
The suspect, who previously ran a martial arts school, immediately opened fire when the officers entered his home. He now faces a murder charge.
The officer had been wearing a bulletproof vest but the shot entered his body through his shoulder, police said.
It was the second serious incident in three months involving the Reichsbuerger group, which does not recognise the legitimacy of the German republic and believes in the continued existence of the German empire or "Reich".
As a result, many refuse to pay taxes and fines owed to the state.
In August, a member of the group -- a former Mister Germany pageant winner -- opened fire on police carrying out an eviction order at his house in the eastern state of Saxony-Anhalt.
The 41-year-old gunman was seriously wounded and three police officers suffered light injuries.
The Office for the Protection of the Constitution, Germany's domestic security watchdog, which keeps tabs on extremist groups, said it had no current figures on the number of Reichsbuerger members.
But an interior ministry spokesman said Wednesday that the movement was seen as "fragmented", with a few hundred members spread throughout the country.