In a press conference in Doha on Thursday, officials said the planning for the hacking of Qatar News Agency started as early as April.
Investigators also reportedly traced the IP address linked to the hacking to the UAE.
Lt. Col. Ali Mohammed al-Mohannadi, head of the ministry's technology division, told reporters that the hacking operation took place in coordination with, and through, "one of the blockading states".
"The hackers had total control of the QNA network, including the related accounts, websites and related social platforms," Lt. Col. al-Mohannadi said.
"This was meant to fabricate and post the false reports, which were attributed to His Highness, the Emir."
Officials said the case has been referred to prosecutors.
The hacking reportedly lasted for about three hours starting late night on May 24 to the early hours of May 25, before the country's media's IT experts managed to take back control of the site.
In a video presentation, the ministry also said that investigators also found out that as early as April, hackers have already "infiltrated" the QNA network "using VPN software", and "scanned the website".
The ministry said the hackers "exploited" a loophole in the network's system, and installed "malicious programs", that were then later used to carry out the publishing of the "false stories".
This comes after the Washington Post reported a few days ago reported that information from US intelligence officials showed that senior UAE government officials discussed the planned hacks on May 23, the day before the alleged hacking occurred.
The hacks and posting took place on May 24, shortly after President Donald Trump completed a lengthy counterterrorism meeting with Persian Gulf leaders in neighboring Saudi Arabia and declared them unified.
Citing the emir's reported comments, the Saudis, the UAE, Bahrain and Egypt immediately banned all Qatari media. They then broke relations with Qatar and declared a trade and diplomatic boycott, sending the region into a political and diplomatic crisis which remains unresolved.