The Malaysian transport agency said that it was misquoted in media reports that it wanted the proposed high-speed railway to end in Johor Bahru rather than in Jurong East in Singapore.
Instead, it actually prefers to have the Singapore-Kuala Lumpur end in Singapore's central business district, said Malaysia's Land Public Transport Commision (SPAD) chief executive Mohamad Nur Ismal Kamal in a press release late last night.
Earlier on Friday, Singapore's Transport Ministry had issued a strongly worded statement to say that it was surprised that the SPAD had stated in media reports that it wanted the HSR to end in Johor rather than in Singapore.
Mr Nur Ismal Kamal had said in a The Edge Malaysia on Monday that "we would prefer to terminate the line at the existing CIQ (customs, immigration and quarantine) complex. However, Singapore wants it to terminate in Jurong East and understandably so."
The MOT said that terminating the HSR in Johor would undermine the objectives of the link.
"Our understanding is that Malaysia views the commercial premise of the KL-Singapore HSR project, and with which we agree, as being based on a direct connection between the two city centres.
"Terminating the HSR in Johor Baru will not achieve this objective," it said.
In a statement released in response to media queries, MOT reiterated that last year, Malaysia had chosen its terminus to be in Bandar Malaysia.
But late last night, the SPAD chief said that he was "regretably misquoted" in the report.
"We would have preferred to terminate the line at the CBD area. This will be closer to Orchard Road than Jurong East. However this is a joint project for the benefit of both countries and hence there has to be give and take," he said.
Last month, Prime Minister Lee Hsien Loong and his Malaysian counterpart Najib Razak announced that Singapore's terminus would be in Jurong East after their annual retreat.
MOT said both countries are also in discussions over the HSR's commercial and operating models.
Singapore has proposed that the domestic transit HSR service, which will stop at the six stations in between Singapore and KL, be operated separately from the express non-stop HSR services between KL and Singapore, MOT said. This will give Malaysia autonomy over the domestic transit services to serve its domestic needs, it added.