Prime Minister Samak Sundaravej was distracted by political turbulence, specifically the opposition movement led by the People's Alliance for Democracy (PAD). As a result, Anupong had free rein over the list of military assignments.
It is now evident that Anupong has practically emerged as the commander of commanders among the three wings of the armed forces.
On Tuesday, while the PAD's final push to oust the government was in progress, Samak and Anupong had a closed-door meeting at Supreme Command Headquarters.
Afterwards Samak's aides said he appeared upbeat and confident that the military would remain his anchor to fight the PAD.
The prime minister failed to get the unconditional support of the military, however. Anupong and outgoing Royal Thai Air Force chief Air Chief Marshal Chalit Phukpasuk made it clear that soldiers would not get involved in crowd-control measures and that the government must rely on legal means to rein in the PAD.
Samak was told that bloodshed would not be tolerated.
Samak and Anupong appear to have forged a deal on a quid-pro-quo basis: no political meddling in the military line-up in exchange for the government getting a new lease on life.
Once the deal was sealed it took less than 15 minutes for the military line-up to be finalised, and Samak submitted the list of appointments for Royal approval on Thursday. The reshuffle will take effect on October 1.
General Apichat Penkitti is slated to succeed outgoing Defence Ministry permanent secretary General Winai Phattiyakul, who will retire on September 30.
General Songkitti Chakkabat is to succeed outgoing Supreme Commander General Boonsrang Niumpradit.
Admiral Kamthorn Phumhiran is to succeed outgoing Navy Chief Admiral Satirapan Keyanon.
Air Chief Marshal Itthaporn Subhawong is to succeed Chalit.
In the Army, Anupong has realigned key positions. General Prayuth Chan-ocha is due for promotion from the position of First Army commander to that of Army chief of staff.
Many have predicted that Prayuth is being groomed as Anupong's successor. It remains to be seen whether the prediction will come true, because General Chavalit Yongchaiyudh was the last Army chief of staff to rise to the top position in the 1980s.
Anupong's personal stamp on the line-up signalled three key changes.
First, plum assignments were evenly spread among the top brass. Anupong, Songkitti and Kamthorn are from Pre-Cadet Class 10, but Apichat and Itthaporn are from Class 8 and Class 11 respectively.
No single class of officers dominates key positions in the three wings of the armed forces. In the past politicians often meddled by pitting one class against another.
Second, Anupong curtailed the domination of Army combat units by Pre-Cadet Class 9 officers, promoted by his predecessor and coup-leader General Sonthi Boonyaratglin.
Third, the armed forces under Anupong's leadership appear to have wiped out the coup legacy. Soldiers are on track for a fresh start.
Before his retirement last year, Sonthi tried to retain his lingering influence via designated officers. Anupong got the endorsement of outgoing commanders to revamp Sonthi's plans.
General Montri Sangkhasap, seen as close to Sonthi, failed to secure a promotion. By the same token, Air Chief Marshal Sukamphol Suwanthat, seen as an ally of former prime minister Thaksin Shinawatra, was unable to secure the Air Force's top job.
With the military reshuffle completed, Samak is left with one daunting task, that of how to pacify the People's Alliance for Democracy, which seems to be demanding his head with a vengeance.