Police and German aviation security officials announced that the no-fly zone will be in place from Thursday until Monday, while the party conference is set to take place on Saturday and Sunday.
More than 4,000 officers will also be deployed for the occasion, according to local newspaper Rheinische Post.
Part of the security concern is that officials expect some 50,000 protesters - including left-wing extremists - to descend upon the city to counter the far-right Alternative for Germany (AfD), with organizers calling for participants to “block” the party conference at a central hotel as a form of “civil disobedience”.
The no-fly zone will apply to almost all flights, including model airplanes and unmanned aviation devices. The only exceptions made will be for German military and police aircraft, as well as for any rescue or emergency aircraft. The ban also excludes flights following aviation regulations that are going exclusively to and from Cologne-Bonn airport, or to and from Nörvenich, where these is an air base.
Police posted an image on Facebook displaying the no-fly zone's boundaries.
Those who violate the ban will be charged under German aviation law for an offense punishable by up to two years in jail, or a fine.
AfD struggle for unity
The far-right party’s conference will also be a test of the AfD’s strength as it has struggled with a bitter power struggle which threatens to scupper its bid to win its first seats in the Bundestag (German parliament) in September.
Once riding high in the wake of Germany's record refugee influx, the upstart party has seen its support plunge into single digits in most polls from around 15 percent half a year ago amid open hostilities between populists and radicals.
In just a taste of the drama expected at the weekend, AfD co-leader Frauke Petry made the bombshell announcement on Wednesday that she would not stand to become the party's official standard bearer heading into the September 24th general election, as she demanded its rival factions adopt a common strategy.
"The image of the AfD keeps getting determined by the uncoordinated extreme provocations of a few representatives who keep surprising the party leadership," she said in a video message on Facebook.
The telegenic public face of the AfD, Petry has become embroiled in infighting as she attempts to cast herself as the moderate, "middle-class" alternative to officials whose outbursts have sparked national outrage for perceived antisemitism and racism.
In Cologne Petry will ask delegates to reject a "strategy of fundamental opposition" to the parties in power and adopt her own pragmatic "Realpolitik" which she argues will attract mainstream voters with the goal of taking the reins of government by 2021.
'Picture of strife'
Petry's decision not to stand as the party's main candidate for the general election - a largely symbolic role - was widely seen as an attempt to avoid an embarrassing showdown at the congress.
"Shortly before their party congress, the AfD is the picture of strife," national daily Süddeutsche Zeitung said.
"That reflects the essence of a party that would like to present itself as middle class but has a method of breaking taboos, provoking and spurning civility."
The AfD has become Germany's most successful right-wing populist party of the post-war period.
Unlike far-right candidate Marine Le Pen in France, its leaders have no foreseeable chance of winning the general election in Germany, where Chancellor Angela Merkel is seeking a fourth term after nearly 12 years in power.
But while all mainstream parties have ruled out working with the AfD, it could clinch enough votes to complicate the post-election maths of forming a ruling coalition.
The AfD was founded as an anti-euro party in 2013, but failed in that year's general election to cross the five-percent hurdle to representation.
Seizing on popular anxiety over the influx of more than one million refugees and migrants since 2015, however, it managed to capture seats in 11 of Germany's 16 regional legislatures.
'Clever as quicksilver'
Following the victories of the Brexit campaign and Donald Trump on waves of anti-establishment sentiment, analysts predicted the AfD would easily enter the national parliament.
But Petry's rise made her both a media star and a red rag for envious party colleagues.
"She is a clever as quicksilver but she's not popular among the delegates because of her blind ambition," Hajo Funke, political scientist at Berlin's Free University, told AFP.
Petry, 41, who is pregnant with her fifth child, has allied herself with hard-right leaders such as Le Pen and Geert Wilders of the Dutch anti-Islam Freedom Party.
But the AfD has lost momentum as the number of new refugee arrivals to Germany has dwindled over the last several months.
The Social Democrats (SPD), junior partners in Merkel's governing coalition, have also managed to claw back some support since appointing a new Merkel challenger, former European Parliament president Martin Schulz.
Schulz has been cast as a maverick in the media and by his party, allowing him to attract voters disenchanted by the Merkel era and squeeze out the AfD's protest-party message.
Funke said Trump's presidency, looming Brexit and the threat to Europe posed by Le Pen have served as a wake-up call for German voters, who may be losing their appetite for radical change.
"The AfD would be fatal for German identity with its strong links to Europe and the country's status as an export nation. That will become even clearer as the election approaches."
With reporting and writing by Deborah Cole, AFP.
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