A German court on Wednesday threw out the results of Berlin's state election 14 months ago and ordered a re-run due to "systematic faults" in how the vote was carried out.

In a ruling with national implications, Berlin's constitutional court found that the German capital, which is one of the country's 16 federal states, had failed to meet basic democratic standards with the September 26, 2021 ballot.

"The linked elections for the state legislature and the (12) district councils for the entire constituency have been declared null and void," the court's chief justice, Ludgera Selting, said.

The exceedingly rare move means that nearly 2.5 million eligible voters will be called back to the polls within 90 days, possibly shifting majorities after a very narrow win for centre-left Social Democrat (SPD) Mayor Franziska Giffey.

Giffey leads a fractious coalition between the SPD, the Greens and the far-left Die Linke.

Any upset could also shift the balance of power in the Bundesrat, the upper house of the federal parliament, which represents the regional states.

Complaints about the fairness of the vote came as soon as election day, which coincided with Germany's general election to decide the successor of then chancellor Angela Merkel -- as well as the city's giant marathon, which blocked off major streets to traffic.

Long queues outside polling stations, missing ballots and chaotic voting hours formed the basis of multiple legal complaints.

Selting said the "frequency and gravity of the electoral flaws" made a repetition a "necessity", slamming "systematic faults in the preparation of the election".

Some districts of Berlin may be called to vote again as well in the general election, which voted in Olaf Scholz as new chancellor, pending a decision by the federal constitutional court.

It is only the second time in German post-war history that a state election was declared invalid, after irregularities were reported in a vote in Hamburg in 1991.