The setback comes as Ruairi Quinn, the education minister, is struggling to get 18 orders to bridge a €400m shortfall in the redress bill.
The order told Mr Quinn it cannot meet the outstanding payments on its €5m promise. It said it has been unable to sell assets.
"The Sisters paid €1m to the Government in 2010, expecting the trust fund to be set up immediately. They have the second payment of €1m ready to pay since 2011 but they cannot release it until the Government puts the trust fund… in place.
"Since the value of their properties has depreciated hugely and the ability to sell property is still severely affected by market conditions — so the nature of their offer has changed," said a statement.
The order said it had offered to waive a demand to recoup €4.9m in legal costs, arising from the Commission to Inquire into Child Abuse. But this claim is considered a separate matter.
This year the order went to the High Court and blocked Dublin City Council’s plans to restrict the development options for key sites.
The order identified three sites — at Sandymount, Harold’s Cross and Walkinstown — it considered surplus to its needs. It asked for these to be zoned for high-density residential buildings or commercial centres. It also said sites at Donnybrook, Merrion and Crumlin would likely come available for sale.
In 2009, it valued its properties at €233m. It had financial interests of €33m and sold €63m of property in 10 years. The order said it needed to set aside €38.6m to care for its 264 sisters.
Meanwhile, the special rapporteur on child protection and child law expert Geoffrey Shannon, said the testimony of women and girls in Magdalene Laundries shows their treatment "constituted slavery".
The Religious Sisters of Charity were just one of a number of orders which ran Magdalene Laundries.