Erick Thohir's first love is basketball but he owns a football club in Indonesia and the media magnate also sees his Serie A purchase as a business venture pure and simple

Internazionale's new owner, Erick Thohir, had an interesting weekend with his club, bouncing on the pitch as supporters sang "If you don't jump you are an AC Milan fan", joking with reporters about signing Lionel Messi and then watching as a Nerazzurri XI lost a friendly 1-0 to a second division Swiss team.

There was a little surprise in Thohir's native Indonesia, where the billionaire is much more of a court-side than pitch-side presence. His investment company has shares in one of the country's leading football clubs, Persib Bandung, but he is a much more visible supporter of the all-conquering Satria Muda team he owns. Basketball, it is generally agreed, is the media magnate's love; football is business pure and simple.

There is nothing pure and simple about football in Indonesia. Since the Soviet Union built the Gelora Bung Karno stadium in 1962 people have tended to take, not give. The Jakarta arena has, when full, the best atmosphere in Asia, rivalled only by Tehran's Azadi. While this face of Indonesian football can take one's breath away, so can what happens out of view.

In the bowels of the stadium are the brown windowless offices of the country's football association, PSSI, linked by quiet windowless corridors where footsteps echo on the shiny wooden floor. From here over the years the stench of corruption and more besides has pumped out to all corners of this vast archipelago.

There are no guarantees that even with the best governance Indonesia would not have lost 1-0 in China on Friday but the Merah Putih (red and whites) would have had a better chance. It is also less likely that they would have all but crashed out of qualification for the 2015 Asian Cup with a third of the group games still to play – one point from four games, albeit in a tough group, says it all.

The 2012 ASEAN Cup – a regional tournament that Indonesia has never won, unlike tiny Singapore with its four titles – ended at the group stage. Much is written about how China struggles in football but the Middle Kingdom is far ahead of Indonesia, the fourth most populous nation in the world. Recent Chinese success at club level has come as investment followed a clean-up of the league. Indonesian fans are not holding their breath.

A senior official at PSSI admitted in May that there were major issues after it was fined $15,000 by the Asian Football Confederation for the latest in a series of crowd disturbances at international games. "Football management in Indonesia is in such a mess at the moment. We aren't able to do anything about things like this," said the spokesman Rudolf Yesayas. "We have much bigger problems."

Those include deadlier levels of violence that can be evidenced in the domestic leagues – during the big game between Persija Jakarta and Persib Bandung in May 2012 three fans were killed – but there is plenty more besides as the country is still trying to recover from years of infighting, incompetence, corruption and cronyism.

The low point came in 2005. The reputation of Nurdin Halid, the PSSI president, was not high even before he was sent down for the first of two prison sentences on charges of corruption. Fifa seemed to care little about enforcing its own rules about criminals or politicians (he was also a member of a major national party) running national associations and Nurdin continued to hold office while in his cell.

Though the 'Jakarta Joker' was finally deposed in 2011, his legacy lives on. Eventually the opposition took power of PSSI and, while the de-Nurdin-ification started (though an increasing number of the old boy's supporters are back in positions of influence), the politics did not stop. The national team coach Alfred Riedl was popular with players and public – during his time in charge of Vietnam more than 80 fans came forward in 2007 offering to donate a kidney on hearing that the Austrian needed a transplant – but in the first act of the new regime he was fired.

By this time there were two federations with two different leagues. Players who left clubs in the official competition to join the rebels were banned by Fifa. A 10–0 thrashing in 2012 at the hands of Bahrain in a qualifier for the Brazil World Cup prompted accusations of match-fixing. Whether foul play was involved or not, this was a demotivated D-team even if the humiliation was A-grade.

In China foreign players have just helped Guangzhou Evergrande become champions of Asia but in Indonesia many imports play with virtual visas, promised but never forthcoming, and phantom pay packets. So numerous are those agents, players and coaches owed money by Indonesian clubs that there have been discussions as to whether to start a Facebook group.

The Indonesia striker Bambang Pamungkas, who stated in March that the country's football was dying, helped to form a players' union in 2012, claiming that 60% of his fellow professionals faced late payment issues – a report in The Times alleged that the total amount owed to players was more than $6m.

Bambang has still not been paid almost a year later and, if it can happen to the country's biggest star – Indonesia's golden boy with almost five million Twitter followers – then what chance do the rest have? The tragic story of Diego Mendieta made headlines around the world last December when the Paraguayan died alone in hospital. He was unable to leave or afford medical treatment after his club had stopped paying him.

In a decade of lows that was the lowest but there is always hope. The Under-19 team recently defeated South Korea 3-2 in qualification for the 2014 Asian Championship to send a Jakarta crowd of 50,000 and a nation wild with delight. Some of the near 70m people in the country under the age of 14 are crying out for a little of the youth development system that the Koreans, who hardly noticed the defeat, take for granted.

That passion means that the politicians will always find the game attractive. For Indonesian fans the major event of 2014 is not the World Cup – the 1938 appearance in the guise of Dutch East Indies, the first ever by an Asian nation, is not looking like being repeated any time in the near future – but the presidential election.

As they say, "Control football and you are on your way to controlling Indonesia." There is not much evidence of anyone controlling anything at the moment and, until that happens, such as Thohir cannot really be blamed if they look to spend their money overseas.