Among them were journalists, human rights activists, and many ordinary people who knew him or had been helped by the 26-year-old editor and independent journalist.
Even as the funeral of the well-known journalist was being held, the office of Kyrgyz President Kurmanbek Bakiev announced that the president will supervise the investigation into the killing of Saipov, who frequently wrote articles critical of the Uzbek government.
Kyrgyz presidential spokesman Nurlan Shakiev told RFE/RL's Kyrgyz Service today that Bakiev has taken the case under his personal control. He said the president "considers this matter important" and that "in order to conduct a thorough investigation right on the scene, he sent Omurbek Subanaliev, the head of the Security and Defense Department of the presidential administration, to Osh."
Saipov was shot dead on October 24 at close range while leaving his office in downtown Osh. The only known witness to the shooting, Iqbol Mirsaitov, is a well-known political analyst and expert on religious groups in the Ferghana Valley. He is being questioned by the police.
Sherzod Yusuf, an RFE/RL Uzbek Service correspondent in Osh, said two bullet cases were found at the scene. He said the first bullet hit Saipov in the leg. "The assailant then approached Alisher and shot him in the head," Yusuf said, citing police sources.
Reported On Uzbek Corruption, Andijon
Among other issues, Saipov covered corruption in the top echelons of Uzbek society and the violation of the rights of Muslims in the Ferghana Valley. He frequently interviewed members of banned religious groups like the Islamic Movement of Uzbekistan and Hizb ut-Tahrir.
Saipov covered the bloody events in May 2005 in the eastern Uzbek city of Andijon, which lies just across the border from Osh. He visited a temporary refugee camp in Kyrgyzstan, writing about the plight of hundreds of Uzbeks who fled Andijon after government troops opened fire on peaceful protesters, killing hundreds.
Saipov, who was an ethnic Uzbek, also criticized the growing cooperation between the Uzbek and Kyrgyz governments and wrote that Uzbek intelligence officers were operating freely in southern Kyrgyzstan.
In August, in his last interview with RFE/RL -- for whom he had once worked -- Saipov voiced concern about the growing threats toward civil society and independent journalists in Kyrgyzstan.
Saipov on October 24, the day he was killed (RFE/RL)
"What is scary about the current events in Kyrgyzstan is that the pressure on religious groups under the pretext of the fight against terrorists could go beyond that narrow group," Saipov said. "Tomorrow, the same may happen to the opposition. [They] or nongovernmental organizations could start facing repression. We are already seeing elements of this: independent journalists are followed by Kyrgyz security agents; NGO representatives have been accused of espionage; and opposition members are accused of cooperation with religious extremists. All of these things concern me very much."
Saipov launched an Uzbek-language newspaper, "Siyosat" (Politics), earlier this year. It immediately became popular among ethnic Uzbeks and others in southern Kyrgyzstan.
Saipov was known to have many visitors to his simple office in downtown Osh, where he worked on "Siyosat" and also contributed reports to the Voice of America (VOA) and some regional news agencies.
Saipov was described by VOA management as "one of the best stringers the [Uzbek] Service ever had." VOA Director Danforth Austin said in a statement that "a professional journalist has paid the ultimate price by doing his job."Uzbek Connection Suspected
Some observers and friends of Saipov's believe that his killing was politically motivated. Saipov had recently told some of his colleagues that he was being followed by men who he believed were Uzbek security agents.
Saipov had also come under heavy attack in the Uzbek state media. Uzbek regional television recently aired a 30-minute program that targeted Saipov's activities and accused him of destabilizing the situation in Uzbekistan.
Shahida Yakub, an exiled Uzbek opposition activist who met with Saipov shortly before his death, told RFE/RL from Osh that Saipov complained about anonymous threats warning him to cease his journalistic activities.
Muhammad Solih, the self-exiled leader of the Uzbek opposition party Erk, had given several interviews to Saipov. Solih accuses the Uzbek government of being behind Saipov's killing. "For several months he has been threatened by [Uzbek President Islam] Karimov's people," Solih said. "I witnessed how Uzbek secret-service agents directly threatened him. Alisher told me about it many times. I have no doubts it is Karimov's doing."
The New York-based Committee to Protect Journalists (CPJ) has condemned the killing. CPJ Executive Director Joel Simon said the CPJ is "shocked and saddened by [Saipov's] brutal murder."
The U.S. Embassy in Bishkek also released a statement condemning the murder. "The people responsible for this killing must be found and brought to justice," it said.
James K. Glassman, the chairman of the U.S.-based Broadcasting Board of Governors, called on Kyrgyz authorities to conduct a "full and complete investigation of the circumstances surrounding this tragedy."
Saipov, who turned 26 in September, is survived by his wife and a three-month-old daughter.
(RFE/RL's Uzbek Service correspondent Shukhrat Babajanov and Kyrgyz Service correspondent Amanbek Japarov contributed to this report from Prague and Bishkek.)