Avas Saipov insisted to RFE/RL in an interview that Karimov ordered and financed the killing of his son, with the assistance of Kyrgyz intelligence officials.
He said Karimov must be held personally responsible for the 2007 shooting, which took place in broad daylight in downtown Osh, in southern Kyrgyzstan.
He alleged that the murderers received help from Kyrgyzstan's Interior Ministry and the State Committee for National Security (GKNB).
"All I know is that Islam Karimov is responsible for Alisher's death; it was done on the orders of Islam Karimov," Avas Saipov said. "People paid by Islam Karimov in Kyrgyzstan -- officers of the Interior Ministry and the GKNB as well as government officials -- provided assistance."
He offered no evidence to support his charges against Karimov or the Uzbek and Kyrgyz security officials.
Alisher Saipov was editor in chief of the Uzbek-language political weekly "Siyosat" (Politics) and was shot dead shortly after leaving his office in October.
Speculation quickly arose suggesting that Uzbek security forces had ordered the killing of the 26-year-old ethnic Uzbek.
Saipov, a Kyrgyz citizen, also contributed to Voice of America and RFE/RL. He wrote about corruption in the upper echelons of power in Uzbekistan and also criticized cooperation between the Uzbek and Kyrgyz governments, writing that Uzbek intelligence officers were operating freely in southern Kyrgyzstan.
Saipov also covered alleged rights violations against Muslims in the Ferghana Valley, which lies in Kyrgyzstan and Uzbekistan as well as Tajikistan. He often interviewed members of banned religious groups like Hizb ut-Tahrir and the Islamic Movement of Uzbekistan.
Saipov reported on the bloody events in May 2005 in the eastern Uzbek city of Andijon. He visited a refugee camp in Kyrgyzstan and interviewed Uzbek refugees who fled Andijon after government troops opened fire on peaceful protesters, killing hundreds.
Before he was killed, Saipov told his friends he had received death threats.
He also was a target of an Uzbek state-media campaign that carried numerous reports about Saipov, calling him an "enemy of the Uzbek nation" and accusing him of destabilizing the situation in Uzbekistan.
A representative for the Moscow-based rights group Memorial has implicated Uzbek intelligence agents in Saipov's death, saying the motive lay in Uzbekistan's presidential election in December 2007.
Memorial's Vitaly Ponomarev told a news conference in the Kyrgyz capital in November that "we have information from certain sources -- on an unofficial level -- that the Kyrgyz special services have received from their Uzbek colleagues information that this [killing] was politically motivated."
Ponomaryov then charged that Kyrgyz investigators had stalled their murder probe.
Avas Saipov said his son's reporting on sensitive issues is the reason politicians in both Kyrgyzstan and Uzbekistan wanted him dead.
"The [Kyrgyz] Interior Ministry and special services collaborated with Uzbekistan's secret service and were involved in [Alisher's killing]," he said. "Why were they interested in this? Because they did not like the truth."
Earlier this month, Saipov sent an open letter to Kyrgyz President Kurmanbek Bakiev. He wrote that the Kyrgyz Interior Ministry's offices in Osh "became the headquarters of Uzbek intelligence" and "some Kyrgyz officials work for Uzbekistan."
Saipov expressed hope that Bakiev would keep his promise and find those responsible for the killing. A day after Saipov's murder, Bakiev announced that he would personally oversee the investigation into the killing, and promised to bring the perpetrators to justice.
Saipov told RFE/RL that he was waiting for the president's response. "Will he respond or not? It is up to him," he said.
"Alisher was a citizen of this country [Kyrgyzstan]. I am also a citizen of this country. I point out that he and I have been citizens who fulfill all the duties of citizenship. As such, I wrote a letter to the president," Avas Saipov said. "[Alisher] was born on this soil, he drank water here. He was a patriot of Kyrgyzstan in the true meaning of the word. Thank God he remained one until his death."
Saipov despairs that his son's murderers will never be found. "Honestly, I don't believe the case will ever be solved," he said, charging that some high-level Kyrgyz officials do not want those who masterminded the murder to be found.
The concerns voiced by the slain journalist's father come amid international criticism of the growing state control over media in Uzbekistan and even Kyrgyzstan.
On June 4, President Bakiev signed amendments to Kyrgyzstan's press law that media watchdogs, including Reporters Without Borders and the Committee to Protect Journalists, have said jeopardize the independence of the country's media.
In Uzbekistan, state-controlled regional television stations in the Ferghana Valley aired a program in mid-June that made sweeping allegations against RFE/RL's Uzbek Service journalists and divulged personal details about their families.
On June 7, Solijon Abdurahmanov, one of few independent journalists working in Uzbekistan, was arrested in his native Nukus in the western part of the country. Abdurahmanov, who is also a former RFE/RL contributor, was accused of drug possession.
RFE/RL Uzbek Service correspondent Hakimjon Husanov contributed to this report from Bishkek