Police in the western city told AFP they have received more than 100 complaints by women reporting assaults ranging from groping to two rapes, allegedly committed in a large crowd of revellers during year-end festivities outside the city's main train station and its famed Gothic cathedral.
Victims blamed men of "Arab or North African" appearance, inflaming a heated public debate about Germany's ability to cope with the nearly 1.1 million asylum seekers the country took in last year.
Authorities have said there is no concrete indication that the perpetrators were asylum seekers who arrived in last year's record influx.
No arrests have been made.
However, critics of Merkel's liberal refugee policy charged that the Cologne assaults proved she was playing with fire without a clear strategy to integrate the mainly Muslim newcomers hoping to settle in Germany.
The right-wing populist Alternative for Germany (AfD) party, which aims to gain seats in three regional elections in March, charged the attacks were "a result of unchecked immigration".
Late Tuesday 200-300 people, according to police estimates, gathered in front of Cologne cathedral calling for better protection for women.
One female demonstrator held a sign reading: "Mrs. Merkel, what are you doing? This is scary."
And Wednesday, a handful of far-right demonstrators from the local Pro NRW group blaming foreigners for a rise in violence was met by a much larger counterprotest of about 150 booing activists.
'Countless weeping women'
"If asylum seekers or refugees carry out these kinds of attacks... it will bring their stay in Germany to an abrupt end," warned Andreas Scheuer, general secretary of Merkel's Bavarian allies, the Christian Social Union, which has demanded she set a strict upper limit of 200,000 newcomers per year.
Attending a CSU meeting at a mountain resort, Merkel said she had no plans to agree to a specific cap but reiterated her position that Germany sought a European solution to the crisis that would lead to a "tangible reduction in refugees".
"We currently have many different approaches among EU member states," she admitted.
Earlier in Brussels, Sweden and Denmark said at an emergency meeting called after they tightened their border controls due to the migrant crisis that they would lift measures, but only after the influx declined.
Merkel has urged a thorough investigation of the "repugnant" attacks in Cologne, which she said required "a tough response from the state".
Witnesses said groups of 20-30 young, intoxicated men out of a crowd of about 1,000 people had surrounded victims, assaulted them and in several cases robbed them.
A plain-clothes policewoman was reportedly among those attacked.
Victims described terrifying scenes in the marauding mob.
Steffi, 31, said she saw "countless weeping women" when she arrived at the station and was hit with a volley of sexist slurs shouted in German as she made her way through the crowd.
"I saw a girl... who was crying, with ripped stockings, her skirt askew -- she was just wrecked," she told the daily Sueddeutsche Zeitung.
"A young guy came out of the crowd and made vulgar comments.
'Can I help you? I know I can help you' he said with a strong accent and made obscene gestures with his hand. When she wanted to get away, he followed her. I told him to piss off."
Justice Minister Heiko Maas warned against scapegoating refugees over the assaults, which he said "appeared to be coordinated".
"No one should exploit the attacks to smear refugees as a group," he told news agency DPA.
Interior Minister Thomas de Maiziere lashed out at Cologne police for failing to stop the assaults, and rejected a claim by police union GdP that the burden of the refugee crisis had meant there was not enough staff to ensure security at railways stations and airports.
He said that foreigners who commit serious crimes "must assume they will be deported".
Faced with accusations of self-censorship of the inflammatory case, which took four days to hit national media outlets, public broadcaster ZDF apologised for delays in reporting on the melee.
And Cologne Mayor Henriette Reker came in for online mockery after saying that girls and young women could avoid trouble of the kind on New Year's Eve by staying over "an arm's length" away from strangers.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.