KABUL — Afghanistan and the European Union on Wednesday announced a deal to send home tens of thousands of Afghan refugees whose asylum applications were rejected in Europe.

The move came as the Taliban’s siege on parts of Kunduz continued for a third day.

“The EU and the government of Afghanistan intend to cooperate closely in order to organize the dignified, safe and orderly return of Afghan nationals to Afghanistan who do not fulfill the conditions to stay in the EU,’’ the 28-country bloc said in an announcement.

Afghanistan’s commitment to accept tens of thousands of rejected asylum seekers was seen as a condition for the aid, some news reports said.

Nearly 200,000 Afghans applied for asylum in Europe in 2015, the second-largest group, after Syrians. The number of Afghan applicants increased more than 350 percent from 2014, according to EU figures, underlining the deteriorating security in the country and the lack of hope among Afghans.

Federica Mogherini, the EU’s foreign policy chief, rejected the reports about conditions for the aid and said the agreement had been signed days earlier in a separate process.

“There is never, never a link between our development aid and whatever we do on migration,’’ Mogherini said.

The refugee deal was signed Sunday, according to news reports. A day before the accord was announced, the Afghan government rejected the idea it had agreed to take back refugees. Asked about reports of an agreement with the EU, President Ashraf Ghani’s spokesman, Haroon Chakhansuri, had said in a text message that “It is absolutely not true.’’

The signed agreement, a framework for cooperation for two years, can be extended. It did not provide information on the number of Afghans to be returned to their home country, but it suggests preparations for a major undertaking.

“Both sides will explore the possibility to build a dedicated terminal for return in Kabul airport and express their willingness to carry out nonscheduled flights at the best convenient time,’’ the announcement said.

The deal is bound to anger many in Kabul, the capital, particularly as the families of many senior government officials live abroad.

Members of the coalition government also seemed to be divided over the terms, with the minister of refugees cautioning “host countries to stop forced repatriation of Afghan migrants.’’

Sayed Ali Kazemi, a lawmaker, said the government’s priority should be restoring security before agreeing to the return of those who braved dangerous waters and spent money to make it to Europe.

“All those who went to Europe — most of them sold all their properties for half price and spent the money to get to Europe, and now when you bring them back, where should they live?’’ Kazemi said.

“Some of the emigrants escaped from war, and the place they come from is now controlled by the Taliban. Where should these people go?’’