The stamp duty holiday, which was introduced in September 2022, meant buyers of properties up to £250,000 have been exempt.
In April, the limit will revert to £125,000 and the first-time buyer threshold of no stamp duty paid on homes up to £425,000 will be removed.
The trade bodies said that as the average property transaction takes around five months to complete, buyers who did not get their mortgage application before the end of October could face higher stamp duty charges.
They added that the Land Registry was also threatening strike action from 21 January over the requirement to be in the office three days per week, which could mean there are delays to the transfer of titles.
AMI and IMLA said conveyancing firms are working through their pipelines and prioritising cases according to mortgage expiry date so buyers do not miss out on a mortgage deal or the stamp duty deadline.

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They noted that lenders are checking pipelines and business development managers (BDMs) are keeping cases flowing as quickly as possible.
The trade bodies said brokers need to contact clients at risk of missing the stamp duty deadline so they can prepare.
Robert Sinclair, chief executive at the AMI, said: “The end of any homebuyer incentive inevitably distorts the market for a period and results in disappointment for those who miss the cut-off point. Managing mortgage borrowers’ expectations is of primary importance at such times as these.
“Brokers and lenders are working hard to complete on as many affected cases as possible before 1 April, but there will no doubt be many [that] don’t beat the deadline. While no one wants to be the bearer of bad news, it is better to have a well-informed client prepared for potential higher buying costs than one who is both disappointed and surprised.”
Kate Davies, executive director of IMLA, added: “Lenders are just as keen as brokers to ensure as many customers as possible can complete on their property transactions ahead of 1 April, but congestion at the conveyancing stage is a real issue, and some borrowers will bear the brunt of higher stamp duty as a result.
“Industrial action at the Land Registry will not help when it comes to transfer of title post-completion, particularly with those less routine cases [that] cannot be dealt with via an automated process. It is more important than ever that we keep the lines of communication open between lender, broker and borrower in the weeks ahead.”