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Pireas was on its way to its next port of call at Tanjung Pelapas in Johor when it collided with Polaris, which was anchored.
A deal was negotiated to suspend the project instead as a cancellation would have entailed a high amount of compensation.
"There are some issues but we are talking to each other," he said.
Singapore said there were five Malaysian government vessels in Singapore’s waters as of 6pm on Wednesday.
On the maritime front, the sides agreed to the establishment of a working group to discuss issues around port limits.
Production at Johor's water plants was disrupted recently by pollution to the river catchment.
Approximately 73 per cent of Singapore's eggs are from Malaysia.
Khaw Boon Wan welcomes Malaysia’s move to de-escalate tensions as 2 ships leave Singapore waters, urges complete withdrawal
But one ship still remains in Singapore's waters as of Wednesday (Dec 12).
Observers say the presence of Malaysian ships is not helpful.
"We will not hesitate to take firm actions to protect Singapore's sovereignty and territory."