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Next year I'll be in Singapore for a month with school, visiting a university as a guest, but will have my hotel in Johor Bahru, Malaysia, and commute by bus CW2 or SJE to central Singapore.

I know there are numerous Malaysian cross-border commuters, who need passports to cross, meaning their passports would get full really soon.

Is there any program to register for that exempts you from having to have your passport stamped four times a day (i.e. 122 stamps in total including the inital entry and final exit from Singapore)?

If there is such a program, is a visa-free foreigner (in both countries) eligible?

UPDATE: Okaaayyy, so I called both immigration authorities today. The Malaysians obviously wanted to know why I booked a hotel in JB, whereby I said that the price difference AFTER adding the transport costs is 2,500 ringgit, which is a lot of money that could definitely go towards food etc. instead, and I'd still have some left over. I also made it clear I used to commute for 1.5-2 hours per direction as a teenager in my home country, and that I'd be happy to send screenshots of the search engine Trivago to show what I mean, but they essentially said it was fair enough.

For the Singaporeans, the instant red flag was the fact that I'm visiting the Duke-NUS Medical school. They said if I'm either a guest for a maximum of 90 days or an actual student for a maximum of 30 days, I don't need a student pass, whereby I said I'm a guest for 31 days. They then asked why the hotel in JB. Said the same thing. They then said they'd be interested in seeing the invitation letter once I get it. I said I'll gladly send it via email if they gave me an address. They finished by saying again that as long as I only do what I mentioned, it's OK.

Regarding the original issue, there seems to be something called MACS (an electronic Malaysian "visa" sticker), and EIACS in Singapore. I'm clearly not eligible for EIACS, but regarding MACS I was advised to contact the application office in Singapore. To save money, I've now emailed them. Those programs apparently exempt you from passport stamps.

Answer to my own question:

I was able to apply for (in Singapore) and obtain a MACS sticker in my passport for 30 ringgit, issued to foreigners other than nationals of Afghanistan, Colombia, Israel and African countries.

Holders don't get their passports stamped in or out of Malaysia, can be processed at dedicated lanes and don't need to fill out the arrival card.

So in the end, as I got MACS on the second day of my visit, I have 2 Malaysian stamps and 63 Singaporean ones (no final exit stamp from Singapore as I used AIG), whilst also not taking too long to cross the border (about 30-45 minutes per direction).

As many of you seemed worried that I'd get stuck in one country or perhaps get deported back to Europe, the crossings were painless, especially on the Malaysian side (admittedly I had MACS, but still).

One morning during my third week, the Singaporean officer did react to the many stamps. He didn't say anything but I saw it in him, whereby I explained a bit nervously that I was an invited guest at Duke-NUS Medical for a month and had my hotel in JB because my own uni hadn't organised accommodation and it was the cheapest solution for me by far. I asked if he wanted the invitation letter from Duke-NUS I had in my rucksack. After two seconds he shook his head and stamped me in (he didn't say a word to me at all in other words)

Other than that, nothing of the sort - the people at the phone hotlines clearly cared much more than the actual officers at the booths.

Next year I'll be in Singapore for a month with school, but will be
staying in Malaysian Johor Bahru and commute by bus CW2 or SJE to
central Singapore.

This is illegal, unless you have a long term multiple entry visa for Malaysia.

Your 90 day exception is for valid tourist (or business) reasons - and is not there for extended stays in Malaysia.

In fact, it is not even a multiple entry visa and recently the government has become more restrictive towards so called "visa runs".

Therefore, this is not recommended. There is a very real risk that you maybe detained, deported and quite likely banned from Malaysia.

Isn't visiting a university (yes, visiting, not studying at) classed
as business? And as for Malaysia, I'm literally only there for
accommodation. Isn't that essentially tourism?

You are not visiting a university are you? You are enrolled in a university; and lying to immigration is immediate cause for denial.

Accommodation is not tourism. You are basically going to university in Singapore and living in Malaysia - which is not allowed under the 90-day visit rules for Malaysia.

No, there is no program that will let you pass daily between Singapore and Malaysia without stamps in your passport. In fact, there is no program that will let you pass at all without the possibility of being refused entry after a couple of weeks (your legal status will be unclear, your ability to support yourself financially is questionable).

The commute you are thinking of doing will take you about 3 to 4 hours each way. That's 6 to 8 hours per day commuting. Your passport becoming full of stamps isn't the real issue here--the plan is simply impractical.

People who are legally resident in one of these countries and legally working in the other do not get their passports stamped, generally. But you are not such a person. Your travel may be seen as "visa running" and denied, since you will be applying to enter as a tourist on one or both sides.