The Danish foreign ministry said in a statement its foreign policy director "made it clear" that Denmark "saw with great concern" those reports about Danish citizens allegedly being registered by Turkish authorities accused of treason because of their political affiliation.
During the meeting, the charge d'affaires said Turkey denied registering Turks living in Denmark based on their political opposition to the government or even having such a registry.
Informing on Turks is only permitted in terrorism-related issues, the charge d'affaires said, according to the Danish ministry statement.
On Saturday, Danish daily Berlingske reported that several Danish citizens of Turkish origin claimed to have been accused of treason by Ankara and placed on a list because of their political views.
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Mustafa Gezen, a high-school teacher in Denmark, had appeared on a TV programme last year criticising Erdogan. He later received an anonymous phone call.
"A man with a heavy Danish accent told me he had recorded the programme. He said he would send it to the Turkish embassy in Denmark," Gezen told Berlingske.
Lars Aslan Rasmussen, a lawmaker for the Social Democrats who has Turkish roots, said he has been contacted by people through Facebook and over the phone saying his name has been sent to the Turkish authorities.
On March 12, Danish Prime Minister Lars Lokke Rasmussen called on his Turkish counterpart Binali Yildirim to delay a visit planned for later this month because of "tensions" between Ankara and the neighbouring Netherlands.
Dutch authorities had refused to allow Turkish ministers to campaign for an April 16 referendum on expanding Erdogan's powers, prompting the Turkish strongman to compare them with Nazi Germany.
"Such a visit could not take place in light of the current attacks by Turkey against the Netherlands. Therefore I proposed to my Turkish colleague to postpone our meeting," Rasmussen said in a statement.