The 20 points and 18 points which were meant to safeguard the rights of the people in both Sabah and Sarawak did not work, causing the people to feel they were cheated.
The ruling party in Putrajaya, Kuching and Kota Kinabalu, which are basically the same, had also been accused of going back on their promises to Sabahans and Sarawakians.
"The federal system did not work in the Malaysian context because of the strong push for political centralisation under former Prime Minister Tun Dr Mahathir Mohammad.
"He had a grand plan to make Malaysia a developed country and he was a man in a hurry.
He absolutely understood that in order to do that he needed unrivalled political power," said Monash University lecturer Prof. James Chin during his presentation at the Borneo Research Council Conference here, Thursday.
Due to the Federal Government's policy, he said, the big political winners since 1963 when Singapore, Sabah and Sarawak together with Malaya formed the Malaysian Federation, are the Muslim communities in both States while the losers are the non-Muslim communities.
"This unhappiness can easily be seen through the social media. If you look at Facebook, there are many pages dedicated to sentiments such as Sabah for Sabahans, Sarawak for Sarawakians and there are also some pages campaigning for Sabah and Sarawak secession from Malaysia.
"This page is quite interesting especially because it had attracted more than 40,000 members!" he said.
Chin stated that the real tension did not arise because the federation did not work well since there had been a certain level of development in both States. Nor is it because 20 Points and 18 Points were the main issues.
The real unhappiness, he said, is really about the export of the West Malaysian political model into Sabah and Sarawak.
"People do not like the fact that this political model is essentially based on racial profile.
It does not work here because of the multiracial component of the society.
"Because of this export of political model into Sabah and Sarawak, many East Malaysians feel that they are losing their unique political, cultural and social environment.
"It is not only unsustainable in Sabah and Sarawak, they are actually changing the whole dynamics of the political, culture and social environment in both states," he warned.
Chin also cited that the unequal treatment of Sabah and Sarawak by Putrajaya had also vexed the East Malaysians.
Unfortunately, he said, this situation will not change as long as the federal political structure does not change since everything depends on the Federal Government.
"If the Federal Government does not change, this unhappiness because of the West Malaysian political model will go on and on and very soon, Sabah and Sarawak will essentially be a mirror of West Malaysia," he said.
Chin also listed down four reasons why East Malaysians are unhappy with the federation to the point of calling for secession.
The expulsion of Singapore, he said, had prompted the people to question whether the federation is still valid since the original constitution specifically stated that in order for a law to be enacted, all four members, Malaya, Singapore, Sabah and Sarawak, must agree.
Adding salt to wound, he added, the Singapore seats were not redistributed, leaving Sabah and Sarawak having only 25 per cent seats in Parliament each instead of one third.
"Borneonisation is also a big issue. Posts were given to West Malaysians instead of the locals. There was a lawsuit regarding this matter but it was thrown out so we cannot find out how bad the situation is at the moment.
"Instead of Borneonisation, there is now a Malayanisation," he said.
The people are also unhappy that Sabah and Sarawak have been lumped together with the other states when in the original constitution, the Borneo states were specifically named together with Malaya and Singapore.
On top of it, Chin said, the people are appalled that the Government did not want to celebrate Malaysia Day which falls on Sept 16 until recently.
"One of the biggest carrots for the people here was the promise that if you joined the federation, you will get better lives. They took the community leaders at the time to West Malaysia.
"There, they spent little time discussing but a lot of time doing what we called 'jalan-jalan', visiting all the highways to show them what they can get.
"But if the promises were true, how come Sabah is very underdeveloped?
Even the government statistics will show that Sabah has the highest poverty rate.
That Pan-Borneo highway? It's just a normal road except maybe between Bintulu and Miri," he quipped.
"There are also suspicions going around now, that the UN commission sent to gather the view of the people prior to Malaysia formation, was fixed. Why? Because the reports in the Cobbold commission and the UN commission were too similar.
"In fact, during the setting up of the UN commission, the British delegation in the UN was working behind the scene, picking up the right people for the commission because they wanted the right result.
"This evidence was found in the archived documents from that period in London by scholars, particularly non-Malaysian scholars, and there is an argument now that perhaps the commission was not as independent as was first thought," he said.