The 45-store bookseller, which includes Books Etc and recently started to sell toys, appointed restructuring specialist MCR as administrator on Thursday, putting 1,150 jobs at risk.
Borders UK had served a notice of intention to appoint BDO as administrator on Wednesday afternoon. But yesterday morning, BDO said it "uncovered a conflict which has prevented BDO from being able to act as administrators to Borders UK."
Phil Duffy, a joint administrator at MCR, said the closure is: "Indicative of the weakening position of book retailers in the current market with competition on bestsellers from supermarkets and the growing strength of the digital and on-line markets in this sector."
MCR said that Borders stores will remain open while it undertakes a review. It is believed that buyers are lined up for around half of the stores.
Borders UK stopped taking orders on its website earlier in the week and a number of publishers stopped supplies over recent days.
MCR said that all outstanding wages for employees have been paid. The administration could lead to a stock liquidation sale before Christmas. In the year to February 2nd 2008, Borders UK's pre-tax losses widened to £13.6m.