Yussuf Hassan, the spokesman for the UN High Commissioner for Refugees (UNHCR) in Kabul, said on Tuesday that conditions were now too "precarious".
The suspension came amid reports of continuing tensions between forces loyal to rival warlords Abdul Rashid Dostum and Atta Mohammad.
The number of refugees affected by this move is not certain but they include people hoping to return to the northern and central provinces of Faryab, Jozjan, Balkh and Samangan.
Factional tensions between rival warlords are known to be high in these provinces despite the recent establishment of President Hamid Karzai's new government in Kabul.
Growing criminality
Both General Dostum, an Uzbek, and Mr Mohammad, a Tajik, support Mr Karzai's administration.
But clashes between fighters from their militias have badly affected the security situation across much of northern Afghanistan in recent weeks.
"The UNHCR is extremely concerned about the escalating violence and the worsening human rights situation in northern and central Afghanistan," Mr Hassan told the Associated Press news agency.
The Uzbek and Tajik militias have clashed sporadically since Northern Alliance forces recaptured the northern city of Mazar-i-Sharif from Taleban units with US assistance last year.
Mohammad's forces say Dostum's militia captured 16 of their Tajik villages 50 miles from Mazar.
Mr Hassan says the violence has been compounded by an increase in criminal activity including robbery, rape and murder across the region.
Cash needed
Meanwhile, the repatriation process faces another intractable difficulty - a shortage of cash.
The UN's World Food Programme (WFP), which provides rations to Afghan refugees sheltering abroad, and recently returned Afghans, said on Tuesday it urgently needed $102 million for its Afghanistan programme.
WFP launched an appeal in April to raise $285 million but has so far received only 64% of the target amount.
The United States contributed $116 million, and the European Union, $7.2 million, a WFP statement said, but among Asian and Arab countries, only Japan had made any contribution.
The WFP says it still needs 175,000 tonnes of food worth $102 million for the Afghan refugees, including the million who have recently returned home.