It looked, at first, like a serious technical glitch. But once staff at al-Jazeera Sports had checked, and then double-checked, they realised something sinister was happening: for nearly 20 minutes the channel's live transmission of the World Cup's opening match between South Africa and Mexico in June was almost impossible to watch because of blank or frozen screens or commentary in the wrong language.

The second half was worse. AJ technicians boosted their signal, only to see the interference grow stronger. Fans across the Middle East and north Africa, in private homes, cafes, restaurants and special screening areas, were furious – and quickly made their feelings clear.

"Al-Jazeera pisses off 300 million Arabs with crappy World Cup reception," fumed one. Another complained: "AJ does not deem it necessary to issue any kind of statement about these 'interruptions'. Nor does it have the decency to issue an apology (let alone a refund)."

Palestinians in the West Bank turned in droves to cheaper Israeli satellite sources. An audience in Dubai trashed a cinema where the matches were being screened. The beautiful game was spoiled from Baghdad to Casablanca. Advertisers demanded extra airtime.

Qatar-based al-Jazeera immediately blamed "sabotage", hinting at "political" motives. Fifa, the international body that organises the World Cup, was "appalled". Egypt, on behalf of Nilesat and Arabsat, both broadcasting al-Jazeera, complained to the International Telecommunication Union, which regulates satellite transmissions. But after the initial outrage, the story faded. No names were named.

Now, secret documents seen by the Guardian reveal what happened. International investigators hired by Arabsat monitored the final between Spain and the Netherlands on July 11, and using geo-location technology – involving a second satellite – traced the jamming in real time to somewhere near as-Salt in Jordan. It remains unclear whether the attack was mounted from a fixed ground station or a vehicle. But it was, in any event, "a sophisticated operation", one expert said.

Jamming involves transmitting radio or TV signals that disrupt the original signal to prevent reception. It is illegal under international treaties. It occurred seven more times during the tournament's biggest games.

It was not hard to find a motive. Before the World Cup al-Jazeera had been negotiating a $7m (£4.4m) rights deal with Jordan TV to transmit 22 of the games on terrestrial channels. But the Jordanians balked at the last minute – complaining that the matches were from the preliminary stages and did not even include Algeria, the only Arab team taking part.

Al-Jazeera's version is that this was a commercial transaction that the Jordanians did not complete. Sources in Doha, the Qatari capital, also ridiculed a request by King Abdullah of Jordan to provide free giant screens for people who could not afford £75 for a one-month subscription package or cards to see the feed.

Middle East analysts say it is hard to escape the conclusion that raw politics lie at the heart of this row.

Jordan, like most Arab governments, heartily dislikes al-Jazeera, which is owned by the fabulously rich Qatari royal family. The channel is anti-establishment and irreverent in an environment where state media fawn over unelected leaders. It also gives sympathetic coverage to opposition and especially Islamist movements. Its critical coverage of the US wars in Iraq and Afghanistan and its sharp focus on the Palestinian issue annoys the Americans and the Israelis. Jordan and Egypt both have peace treaties with Israel that are unpopular in both countries.

Nearly every Arab regime has had its spats with al-Jazeera, so the initial assumption in Doha was that the jamming might have been carried out by Egypt, Libya, or Jordan.

"The whole idea of al-Jazeera's exclusive control of the World Cup annoyed a lot of Arab leaders who saw it as a way to make them crawl to the emir of Qatar to let them have the games for free," said Mamoun Fandy, an Egyptian political scientist and the author of (Un)civil War of Words, a book on the channel.

But it was Jordan that acted. King Abdullah had sent his media adviser, Ayman Safadi, to negotiate the rights deal with al-Jazeera, and there was trouble when it did not go ahead. An official complained to the Jordan Times that the network's stance was "based on a political agenda and has nothing to do with commercial or any other purposes".

Al-Jazeera, he added, was "punishing the Jordanian people, who have the love of sports in their blood".

Abdullah, a keen football fan, was furious. "The king was very angry," one source said. "He wanted to bribe his people with the World Cup at Qatar's expense. But al-Jazeera is a business. The message of this jamming is that 'there is no limit to what we will do if we don't like you'. It shows that even football can't escape politics."

Fandy agrees. "It's a political message. The Jordanians are saying: 'Screw with us and we will screw with you'."

The Jordanian government declined to comment on the allegations when approached by the Guardian.

The jamming was a highly damaging blow to al-Jazeera's reputation – one reason why the channel prefers not to discuss it in public. Fifa spokesmen refer questions about it back to Doha. And the Qatari government prefers silence, because of the embarrassing political and diplomatic ramifications. This episode, media analysts suggest, can hardly help Qatar's bid to host the World Cup in 2022.