In April, 10 Pakistani Taliban militants were handed down 25-year jail sentences by an anti-terrorism court after holding them guilty.
However, sources have now confirmed to the BBC that only two of the men who stood trial were convicted.
The secrecy surrounding the trial, which was held behind closed doors, has raised suspicions over its validity.
Saleem Marwat, district police chief in Swat, where the attack on then 15-year-old Malala took place, separately confirmed that only two men had been convicted.
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Ahmed claimed that the original court judgement made it clear only two men had been convicted and blamed the confusion on misreporting.
The acquittals emerged after reporters from the London- based Daily Mirror attempted to locate the 10 convicted men in prisons in Pakistan, the report added.
The trial was held at a military facility rather than a court, a Pakistani security source told the BBC, and was shrouded in secrecy. Anti-terrorism trials in Pakistan are not open to the public.
Authorities also did not say when and where the men had been arrested or how they were linked to the attack, or explain the charges against them.
Malala was targeted by Taliban gunmen while she was returning home from school in the town of Mingora by bus which the gunmen boarded and asked for her by name before shooting her in the head.
She was treated for her injuries in the UK and currently lives in Birmingham with her family due to Taliban death threats.