Nadhim Zahawi MP last month told the House of Lords Secondary Legislation Scrutiny Committee that the commercial system Link Maker is stepping into the breach. It is now believed to be used by all local authorities.
Meanwhile charity Coram, which had run the statutory register via CoramBAAF between 2016 and the March 2019 closure, believes Link Maker is not set up to fill the gap.
Recent legislation changes remove the requirement on local authorities to record children who are without a match after 90 days.
According to Coram, without the register, which was supported by free specialist matching service Adoption Match, the hardest-to-match children may be deprived of the last hope of finding a family - a claim which Link Maker has said Coram has put in a "misleading" way.
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Coram's concerns have been echoed in a committee report on the changes, which are to be debated in the House of Lords next week.
In a letter to committee chairman Lord Trefgarne dated 23 May, Coram's chief executive Dr Carol Homden, states: "This provision has now been lost so there is a new risk some children will go unseen.
"In the last year alone, matches were found for 277 of the hardest to place children in this way and through exchange days bringing professionals together with adopters from across the country.
"These children could all have been ‘advertised' on the commercial system which provides the solution for many, but they were not ‘chosen'."
Link Maker, which charges local authorities between £5,000 and £10,000 for an annual subscription, accepts it does not itself offer a matching service.
It does not do so because, it claims, this is best carried out by social workers "who know the children best and have a statutory duty to try to match them".
The company's chief executive Andy Leary-May said: "Carol Homden made an assertion that may be misleading to those considering this key question."
He said that by contrasting Coram's specialist matching service with his system, Homden seemed to "suggest that Link Maker does not support ‘child-led' searching and therefore may not meet the needs of ‘harder to place' children".
He added: "Our understanding is that those seeking matches for harder-to-place children achieve matches more quickly, and more efficiently, when searching themselves directly, and this is in part why Link Maker has been preferred."
Homden responded: "Link Maker is an excellent system and long may it continue, but it isn't a matching service.
"Children need all of the chances for their future and for some this register service was their last chance.
"The number of matches made quadrupled over the last three years and the risk now is that some children will fall through the gap."
In his own letter to the committee, Zahawi suggests that Coram is setting up a new matching service.
Coram confirmed that the minister would have been referring to its venture Be My Family, but added that this was a paid support service for helping local authorities with recruitment for matching.
It is "not a direct replacement for the Adoption Register and doesn't include a matching database", said the charity.
Homden added that she hoped the charity's continued efforts via its adoption exchange days, would "help mitigate the impact for around half of those previously matched".
Lord Russell of Liverpool, who has declared an interest as a governor of Coram, has tabled a "regret motion" on the changes to the regulations, for debate in the Lords on 18 June.
Lord Russell will move that the Secretary of State has "failed to put forward satisfactory evidence to justify these decisions, to offer a timetable for and clarity about a replacement for the register, and to explain how Her Majesty's Government intend to mitigate the risk of reduced provision for children who may be harder to place".
However, even if carried, the motion would have "no effect on the legal validity of the instrument", the House of Lords confirmed.