Farid al-Deeb said the former president had imposed a curfew on the afternoon of 28 January and transferred responsibility to the head of the army.
The police or interior ministry could therefore not have been ordered to open fire on demonstrations, he argued.
Mr Mubarak could face the death penalty if convicted of killing protesters.
The former Interior Minister, Habib al-Adly, and six senior policemen are co-defendants.
Mr Mubarak's two sons, one-time heir apparent Gamal and Alaa, are facing separate charges of corruption with their father in the same trial.
Army 'does not lie'
On Wednesday, Mr Deeb told the court: "Mubarak used his constitutional power and issued an order imposing a curfew across Egypt and put the army in charge of security from 16:00 on 28 January."
"Therefore, it does not make sense that police ordered the killing of protesters. The police did not have the jurisdiction or authority to issue any orders since the authority had been transferred to the head of the army," he added, according to the AFP news agency.
But Mr al-Deeb said he was not accusing the army of ordering the killings.
He was quoted by AFP as saying that the army had denied ever firing on protesters, and that he believed "the army, because it does not lie".
The defence began arguing its case on Tuesday.
The former president was wheeled into the court on a stretcher, but was later reported to have sat in a wheelchair.
Lawyers for the 83-year-old had earlier been quoted as saying Mr Mubarak was unable to sit up due to the risk of stroke.
The trial against Mr Mubarak began last August and the case against him culminated in early January, when chief prosecutor Mustafa Suleiman argued it was impossible that Mr Mubarak had not ordered police to open fire on protesters, leaving more than 800 dead.
But the BBC's Jon Leyne in Cairo says prosecutors have complained of a lack of co-operation from the interior ministry in producing evidence, and the case has been weakened by a key witness changing his testimony.
The police or interior ministry could therefore not have been ordered to open fire on demonstrations, he argued.
Mr Mubarak could face the death penalty if convicted of killing protesters.
The former Interior Minister, Habib al-Adly, and six senior policemen are co-defendants.
Mr Mubarak's two sons, one-time heir apparent Gamal and Alaa, are facing separate charges of corruption with their father in the same trial.
Army 'does not lie'
On Wednesday, Mr Deeb told the court: "Mubarak used his constitutional power and issued an order imposing a curfew across Egypt and put the army in charge of security from 16:00 on 28 January."
"Therefore, it does not make sense that police ordered the killing of protesters. The police did not have the jurisdiction or authority to issue any orders since the authority had been transferred to the head of the army," he added, according to the AFP news agency.
But Mr al-Deeb said he was not accusing the army of ordering the killings.
He was quoted by AFP as saying that the army had denied ever firing on protesters, and that he believed "the army, because it does not lie".
The defence began arguing its case on Tuesday.
The former president was wheeled into the court on a stretcher, but was later reported to have sat in a wheelchair.
Lawyers for the 83-year-old had earlier been quoted as saying Mr Mubarak was unable to sit up due to the risk of stroke.
The trial against Mr Mubarak began last August and the case against him culminated in early January, when chief prosecutor Mustafa Suleiman argued it was impossible that Mr Mubarak had not ordered police to open fire on protesters, leaving more than 800 dead.
But the BBC's Jon Leyne in Cairo says prosecutors have complained of a lack of co-operation from the interior ministry in producing evidence, and the case has been weakened by a key witness changing his testimony.
