MYANMAR'S president Thein Sein has launched a palace coup within the ruling party to shore up his support and end the presidential hopes of his rival, the speaker of the lower house Thura Shwe Mann. It also comes immediately after a massive shakeup in the army hierarchy – with nearly two hundred senior officers having retired or in the process of stepping down – and a major reshuffle in Cabinet.

This appears to be the final act in a battle between the two key giants in the Union Solidarity and Development Party (USDP) that has intensified in the last few months – becoming increasingly public. The latest move though seems to have been orchestrated by the army, and the former military leader, Than Shwe, may also have been behind it.

In a midnight raid on the USDP headquarters in the capital Naypyidaw, led by several Cabinet ministers, the police surrounded the Union Solidarity and Development Party's offices and prevented anyone from leaving, according to a source inside the building. Shwe Mann, the acting chairman of the party – as under the country's constitution Thein Sein could no longer run the party after he was elected president – and the general secretary Maung Maung Thein were removed from their official positions in the party.

The vice chairman Htay Oo has been appointed temporary chairman. He has been increasingly critical of Shwe Mann over the past year, and is known to be close to Than Shwe. He has also distanced himself from Thein Sein – being an ardent supporter in the first two years of his presidency – but has become increasing concerned about Thein Sein's indecisiveness over the past year or so. "He is regarded as the man in the middle," said senior party officials on condition of anonymity. Htay Oo is now joint party chairman with President Thein Sein.

But it remains unclear where this leaves the president and his chances of seeking a second term in office. What is clear is that this was timed to make changes to the party's list of constituent candidates and the rejection of the retiring military officers. Today (Friday) is the deadline for the party lists to be submitted to the Union Election Commission – and then there is a further week when changes can be made.

"What is certain is that this 'coup' will have a significant impact on the country's transition to democracy," said political commentator and former political prisoner, Dr Than Myo Thein.

With elections less than three months away, the struggle is over who should run for the party in the forthcoming polls – and in which constituencies. Maung Maung Thein was in charge of the selection process and Shwe Mann – as the acting Chairman – approved the lists. Prominent ministers were left out, and Thein Sein declined to run for parliament because of health concerns. But the main concern was the party's rejection – under Shwe Mann's instructions – of the former military officers who wanted to join the party and run for parliament. Earlier this week, 149 senior officers retired from their army posts to enter politics. But at the party convention on Wednesday, only 59 of the former army officers were accepted as candidates.

Tensions between USDP factions and the military surfaced in June, when the party backed a motion – on Shwe Mann's initiative – that would have ended the military's de facto ability to veto constitutional amendments, as any change needs at least 75 percent of parliament to approve it, and under the constitution the military have 25 percent of the seats. Shwe Mann has taken several swipes at the military in parliament in the last few months, causing them to take offence. But it has been his blocking of the retiring senior officers entry into the USDP that has precipitated the recent showdown.

In the past, these military officers would automatically have joined the USDP – as most of the ministers and MPs did before the 2010 election, including both Thein Sein and Shwe Mann. This is part of the usual military shake up and annual promotions at this time of year. But this year has added urgency and significance because of the upcoming elections.

Naturally this batch of officers expected to join the USDP, become election candidates, and some to become ministers in the next Cabinet or be appointed Chief Ministers in the fourteen state and regions. But only a third of them were welcomed into the party, according to sources close to the army. Fearing he would lose control of the party, Shwe Mann blocked most of them from becoming party members, and entering politics under the USDP flag.

Within the army at the very top Shwe Mann has begun to be openly called a traitor, according to military sources. "The last time that happened," said a former military officer, who declined to be identified, "was [former intelligence chief and prime minister] Khin Nyunt before he was arrested and put under house arrest [in October 2004]." The speaker has obviously broken unwritten laws of the army – especially in trying to change the constitution.

The USDP MP Thura Aung Ko – who recently had a heartache – said the divisions within the party were irreconcilable. The current showdown is obviously the result of a movement within the party to get rid of Shwe Mann, once and for all. "When it happens,

it will be the night of the long knives," said a source in the president's office a few weeks ago, on condition of anonymity. So now that coup has been launched.

Former senior general Than Shwe reportedly sent a message shortly before the USDP Central Committee meeting in June warning them to keep the party from fracturing. "You three [Thein Sein, Min Aung Hlaing and Shwe Mann] must learn to cooperate well," he reportedly said. "or I may have to take things into m own hands," he allegedly said.

At present Thein Sein – with the army chief Senior General Min Aung Hlaing's support – certainly has the upper hand. But he is by no means sure of emerging as the president after the elections. Some analysts also fear that this coup may mean the elections will be delayed. "The polls on 8th November are almost certain to be postponed now," said Dr Yan Myo Thein. And under the constitution, the electoral commissioner can delay them up until the end of January 2016 – five years after parliament first met and elected Thein Sein as president for his fist term in office.

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The writer is a specialist on Myanmar and a former BBC World Service News Editor for the Asia region.