Briefing reporters, he said Israel estimates Assad still has "between one and three tons" of chemical weapons.
The assessment was confirmed by two other Israeli defense officials.
In a three-part report, the professor has concluded that the White House did not base its claims on "concrete" evidence and says that the attack could have been perpetrated by the rebel forces fighting against Assad's rule.
Israel has largely stayed out of the civil war raging in its northern neighbor.
The missile strike was the first direct U.S. military action against Assad's forces since the start of Syria's civil war six years ago and precipitated a downward spiral in ties between Washington and Moscow.
Following Russia's intervention in September 2015, Israel and Moscow opened a hotline to coordinate military activity in Syria.
Syria agreed to give up its chemical weapons arsenal to avert US strikes in September 2013, following a chemical weapons attack in the Damascus suburbs in August that year that killed hundreds of people and sparked worldwide outrage.
"We know beyond doubt that two Sukhoi-22 aircraft took off from Shayrat airfield where we know that chemical weapons are stored", Johnson said. In August 2013, the regime also used sarin in the suburbs of the capital Damascus, killing 1,429 people, including 426 children.
The statement points out that an actual WMD attack in Khan Sheikhoun is unlikely given that "there are no requests for special medicaments, antidotes, [or] decontaminants made by civilians or pseudo rescuers".
A fact-finding mission from the Organization for the Prohibition of Chemical Weapons, an global watchdog, is investigating the incident and is expected to issue a report within two weeks.
"It is my belief, though I stress no such decision has yet been taken, that were such a request to be made in future, were it to be a reasonable request in pursuit of similar objectives, then I think it would be very hard for the United Kingdom to say no", Johnson said.
Samples from 10 victims of the April 4 attack on Khan Sheikhun analysed at four laboratories "indicate exposure to sarin or a sarin-like substance", said Ahmet Uzumcu, head of the Organisation for the Prohibition of Chemical Weapons.