Built as part of the Southern Integrated Gateway project on the former site of the Lumba Kuda flats, Kampung Bukit Chagar, the building occupies an area of 232,237 square metres (2,499,780 sq ft), making it the largest CIQ complex in Malaysia.

Originally even after Johor and Singapore were designated as separate British protectorates, and the Johor–Singapore Causeway was built to accommodate land access between both states, no border control was established between them.

However, checks would be done periodically due to extraordinary circumstances, such as the Malayan Emergency, but otherwise the citizens of both sides were free to roam between the regions without many conditions.

When the border control was first established between both Malaysia and Singapore, the only necessary document was mainly only identity cards issued by both governments to pass through and both countries still retained joined visa issuance to visitors.

While the original plan to make Skudai Highway part of North-South Expressway was scrapped due to Johor Bahru's town developments restricting the road upgrades, a toll plaza was introduced on the CIQ complex and started charging motorists that passed through the Causeway, in or out.

In 2002, accommodating to growing need for a better, smoother border crossing condition, the Southern Integrated Gateway was proposed, combining a new CIQ complex, new bus and train stations as well as new bridge to replace the Malaysian side of the Causeway.

However, despite some groundwork already ongoing, the Tanjung Puteri bridge plan was cancelled by the federal government, now under Abdullah Ahmad Badawi as Prime Minister, citing costs and diplomatic issues.

The power outage created traffic jam in Singapore side of the Causeway and Immigration and Checkpoints Authority warned travellers of "tailback from Malaysia".

All foreign-registered vehicles embarking from the Singapore Woodlands checkpoint can purchase a TnG card at an old building on the left side of the causeway before approaching Johor.