some facts regarding berthing and custom clearance
There are 2 marinas here, Puteri Harbour and Danga Bay. However, Danga Bay has now closed permanently and it is no longer possible to berth here. The area will be absorbed into the huge satellite residential development that has been taking place in the area for the last 2 years.
All yachts requiring clearance here must ensure they fly the Q flag, otherwise they may be fined.
Yachts coming from Sebana and other ports in Malaysia also have to do harbour clearance here.
Clearance can be completed at Puteri Harbour Marina.
Immigration is at the causeway and the Harbour Master (in Jabatan Laut), 1km along the waterfront from the anchorage, towards the causeway, as is the Customs office.
Yachts aiming for Senibong Cove Marina would be advised to first stop at Pengileh to clear in. There is a marina there but it's not suitable for a cruising yacht. Anchoring just outside is tenable, and all the officials are in the same building so clearance is quick and efficient. You then proceed around the east/northeast side of Singapore to Senibong or the anchorage east of the causeway. You will see Singaporean police boats monitoring the border pretty consistently along this 20NM stretch.
Customs is only required for outward clearance and issue of Port Clearance after clearing out with the Harbour Master.
Immigration outward clearance is not required if stopping at further Malaysian ports on the Penninsula. Clearance is required if heading to Sarawak or Sabah on Borneo.
Many nationalities will receive a new entry stamp, which is good for a three months stay in Malaysia, each time they return across the causeway from Singapore or on arrival. However, it's best to do up-to-date research on your own situation first, as the list of permitted nationalities is ever-changing.