Since the beginning of 1947, tensions between the Hòa Hảo followers and the Communists escalated. In February 1947, a Reconciliation Committee, or Ủy ban Hòa giải, was formed to prevent further incidents between Hòa Hảo units and Việt Minh forces. Nonetheless, bloody incidents and clashes continued in the Long Xuyên area.
In late March and early April 1947 the Communists repeatedly attacked Hòa Hảo positions. Paradoxically, Huỳnh Phú Sổ was still technically on the Southern Administrative Committee, holding the post of “special member.” He received an invitation from Trần Văn Nguyên, the Việt Minh political delegate for the Western provinces, to attend a committee meeting to review the situation. Nguyên and the Việt Minh local commander Bửu Vinh wanted Huỳnh Phú Sổ to come to Tân Phú hamlet, Đốc Vàng Hà village, Long Xuyên province to discuss plans for a bilateral cease-fire.
Prophet Huynh Phu So, during a trip to the western provinces of southern Vietnam to preach and to promote agricultural expansion.
At 7 AM, on April 15, Huỳnh Phú Sổ sailed towards the Tân Phu areá. Five bodyguards, three boatmen and his secretary, Huỳnh Hữu Thiện accompanied the Hòa Hảo leader. Around 8 AM, the boat reached the area of Ba Răng market where Huỳnh Phú Sổ met Trần Văn Nguyên. They also held an impromptu meeting. Huỳnh Phú Sổ addressed the crown and urged it to stop clashes between Hòa Hảo and Việt Minh troops so as to reinforce solidarity against foreign aggression. Then Huỳnh Phú Sổ and Trần Văn Nguyên had lunch, and around noontime, they went to Tân Phú hamlet where they announced a joint statement calling for bilateral reconciliation and an end of violence.
Huỳnh Phú Sổ spent the following night at a house of one Hòa Hảo follower, then around 7 AM on April 16, he renewed negotiations with Trần Văn Nguyên. As a result, the Việt Minh commander sent one of his officers, Ngô Trung Hưng, with a mission to reconcile the warring factions and prevent further clashes.
After lunch, Huỳnh Phú Sổ had a rest inside his boat, Bửu Vinh arrived and sought an urgent meeting with the Hòa Hảo leader. Bửu Vinh claimed that activists of the Social-Democratic Party had just murdered some Việt Minh supporters in Lấp Vò and urged Huỳnh Phú Sổ to go there immediately to investigate the incident. The Hòa Hảo leader said no and suggested going together. Bửa Vinh rejected the idea on the grounds he would have needed an armed unit to guarantee his security. Huỳnh Phú Sổ retorted that since he had arrived in the Việt Minhs stronghold with just a few of his people, there was no reason for Bửu Vinh to demand more bodyguards.
Subsequently, Bửu Vinh invited Huỳnh Phú Sổ to his office to discuss the planned joint trip. Suddenly, Trần Văn Nguyên came in and gave the Hòa Hảo leader a piece of paper, which said that Huỳnh Phú Sổ had been invited to attend an extraordinary meeting of the Southern Administrative Committee in the 7th military zone. However, Huỳnh Phú Sổ rejected the invitation and refused to leave the Mekong Delta, arguing that his personal presence was needed to oversee the process of reconciliation.
In the evening, Huỳnh Phú Sổ once again came to Bửu Vinhs office. As the Hòa Hảo leader sat inside and spoke with Bửu Vinh, his four bodyguards stood on alert out of the house. Ten minutes later, around 7.30 PM, eight Việt Minh soldiers divided into four teams of two suddenly attacked Huỳnh Phú Sổs bodyguards. Three guards were stabbed and died instantly yet the fourth man, Phan Văn Tỷ, escaped and opened fire. In the meantime, one of the Việt Minh soldiers was also stabbed incidentally. Inside the office, Huỳnh Phú Sổ turned off the light and nobody saw him any longer.
Huỳnh Phú Sổs secretary and three boatmen also escaped and reported his arrest to the Hòa Hảo leaders in Phú Thành. Yet when the adherents urgently prepared an armed assault against the Việt Minh hideout, unexpectedly a messenger arrived and brought a letter from Huỳnh Phú Sổ, addressed to Trần Văn Soái and Nguyễn Giác Ngộ.
The letter said: “As I negotiated with Bửu Vinh, a disaster suddenly befell. We both escaped death while investigation of the incident continues. I am not aware whether my bodyguards died or escaped. In the event any of them reach you and report that I was either detained or killed then you should not believe them and put the troops on alert. I forbid making the incident public or sending troops to rescue me. The troops should remain where they are. I will investigate the incident in partnership with Bửu Vinh and I will return afterwards. This order should be observed precisely. 9.15 PM, April 16, 1945. Signed: Huỳnh Phú Sổ.” Vương Kim, 1975, p.177.
Huỳnh Phú Sổs adviser Mai Văn Dậu checked both the handwriting and the signature. He concluded that the letter was written by the Hòa Hảo leader. Therefore the Hòa Hảo adepts followed the order in a pious hope that Huỳnh Phú Sổ would have returned on the next day. However, since April 16, 1947 Huỳnh Phú Sổ has never been seen again. Yet because the Hòa Hảo leaders had the order to maintain peace as long as possible, they took no action until the following month.