Amir was alleged to have committed the offence on one Norikoh Saliwah in a moving lorry headed from Kota Marudu town to Langkon, at Km 2.8 along Jalan Kota Marudu-Langkon, between 11am and 12.30pm on Nov 25, 2012.
The offence under Section 304(b) of the Penal Code carries a jail term of up to 10 years, or with a fine or both, on conviction.
In acquitting Amir, Ishak said the prosecution had failed to prove a prima facie case against him.
Ishak, however ordered Amir to be referred to the Immigration Department immediately for further action following an application by the prosecution because Amir's passport had expired during the remand period.
Amir, who was then whisked away to the court cell, said he was satisfied with the decision and looked forward to have his passport renewed.
In delivering his ruling, Ishak, among others held that all the prosecution's three witnesses - Arwin Amin, Turagis Lamun, Nina Natasha Bigong were neither able to supply the registration number of the lorry nor were able to categorically state whether Amir was either the driver or the passenger of the lorry at the time of the incident.
"Nevertheless all three of them provided the description of the lorry, to my understanding referred to the lorry owned by the accused (Amir). Their description also matched one that was furnished earlier by Bibianah Saliwa (Norikoh's sister) regarding the lorry in which her sister, the deceased boarded.
"Turagis in particular was able to provide a highly detailed description of the lorry that he had witnessed. The features described include a white body, a black wall É and a yellow and read rear sticker at the back of the lorry.
"Furthermore, in his testimony, Turagis had also stated that he could see two persons in the lorry before the girl swung open through a window at the back of the cabin.
"This description appears to be consistent with the lorry and the photograph he identified.
Furthermore, Turagis, Arwin and Nina identified the said lorry from the photograph shown to them in court.
"To further strengthen this, Turagis has been able to identify the particular lorry among the lorries parked at the police station at that time. Therefore, the combined testimony of these three witnesses alone had in my mind been sufficient to establish a prima facie case for the allegation that the deceased had indeed fallen from the lorry belonging to Amir, which was the one identified by these witnesses.
"However, the odd decision subsequently made by the prosecution to call on Mohd Ibrar (a Pakistani) to identify the said lorry, even when a prima facie case could have already been established by the prior three witnesses served to compromise my conviction," said Ishak.
He said the last eyewitness offered by the prosecution - Mohd Ibrar testified that Norikoh died as a result of falling from a different lorry.
"According to Ibrar, although he was nearly 10 metres away from the lorry as he witnessed the deceased falling from the lorry onto the ground, in his recollection, the lorry was not the same as the one shown in the photograph, which had been identified by the prior three witnesses.
"Ibrar maintained his assertion that it was not the same lorry throughout the examination-in-chief and cross-examination, attesting that the lorry that he witnessed was old, had an old black rear door and no yellow and red rear sticker at the back," said Ishak, adding that it clearly contradicted the testimony of the previous three witnesses.
Ishak also held that he did not have the opportunity to observe the demeanour of Mohd Ibrar, whether he appeared to be telling the truth based on his overall demeanour.
"From the notes of the proceeding, there was nothing to show that this prosecution witness was impeached on his testimony nor was he treated as hostile witness nor was he challenged by the prosecution that he is lying or not telling the truth.
"Furthermore, neither DNA nor finger print matching those of the deceased was found on the lorry belonging to the accused that could conclusively prove that the deceased had been in the said lorry on that day.
"Had the Deputy Public Prosecutor sought to dismiss the testimony of her own witness, Mohd Ibrar or successfully impeached his contradictory testimony, then my decision should have been very different," said Ishak in acquitting and discharging Amir from the charge without calling him to enter his defence.
Ishak had earlier held that it must be noted that he did not have the opportunity by himself to see and to hear the prosecution's witnesses and that his ruling was based on his reading and examination of testimony of witnesses, note of proceedings as well as the submission by both the prosecution and the defence.
The prosecution had called 40 witnesses to testify before the previous judge Duncan Sikodol, who is now with the Attorney General's Chamber in Putrajaya.
Meanwhile, DPP Raja Zaizul Faridah Raja Zaharuddin said the prosecution would be filing an appeal to the High Court against the decision.
Counsel Peter Marajin, who is holding a watching brief for the girl's family, said the prosecution's decision to appeal was a very good one for the sake of justice.
Amir was represented by counsel Dato Rakhbir Singh.