Chief Superintendent John McBride said the Scottish Government's plan could also cut the effectiveness of railway policing.
BTP's divisional commander for Scotland said the force's specialism was at risk, with dozens of officers expected to leave if the merger goes ahead.
Mr McBride, who gave evidence to Holyrood's justice committee on behalf of the BTP Superintendents' Association, said when Police Scotland officers were involved in rail incidents, it took at least 50 per cent longer for them to to investigate and get trains running again.
He said the merger would risk the innovative and disruption-minimising way in which BTP dealt with the main crimes on Scotland's railways - trespass and vandalism, cable theft, level crossing abuse, graffiti, and people with mental health issues and deaths.
This included being the first force to identify and highlight the widespread impact of metal theft after copper signalling cable thefts caused major disruption to trains.
Mr McBride said he agreed with Police Scotland Assistant Chief Constable Bernard Higgins that the merger would be massively complicated and cause a "level of disruption".
He also said he was not convinced the railways could be policed to the same standard immediately after the planned merger in April 2019 "or any time soon after that".
He said: "It could be quite disruptive."
Mr McBride said the uncertainty caused by the merger proposal had also caused "significant angst" among staff.
He said up to 40 staff "near the end of their service" might choose to leave.
"That specialism will take a hit right away."
Nigel Goodband, chairman of the British Transport Police Federation, which represents rank-and-file officers, said the Scottish Government had only asked for views about the best way BTP should be integrated with Police Scotland, rather than whether it should happen, which he said was "very concerning".
Alisdair Burnie, of the Transport Salaried Staffs' Association, which represents some BTP staff, said: "We do not understand why they are trying to fix something that's not broken."
Mick Hogg, Scotland organiser of the Rail, Maritime and Transport Workers union, said it had not ruled out taking industrial action to retain BTP.