Dr David Rosser said she was making good progress, but has a long way to go and is not out of the woods yet.
The 14 year-old schoolgirl was shot in the head by a Taliban gunman for her campaign for girls' education.
Pakistan's president described it as an attack on "civilised people".
Speaking in Azerbaijan on Tuesday, President Asif Ali Zardari said: "The Taliban attack on the 14-year-old girl, who from the age of 11 was involved in the struggle for education for girls, is an attack on all girls in Pakistan, an attack on education, and on all civilised people."
'Right direction'
Malala was flown to the Queen Elizabeth Hospital in Birmingham on Monday night for treatment.
Security is tight at the hospital, with a police presence in place to deal with any unauthorised visitors.
On Monday night a number of well-wishers turned up hoping to see her but were turned away by West Midlands police.
Dr Rosser described the incident as "irritating", but said the hospital and its partners are "comfortable with security arrangements".
The Taliban have threatened to target Malala again and she was given tight security for her journey to the UK.
Dr Rosser said the team of specialists working with her have been pleased with the teenager's progress.
"There's a long way to go and she is not out of the woods yet... but at this stage we're optimistic that things are going in the right direction," he added.
Once Malala recovers sufficiently, it is thought she will need neurological help as well as treatment to repair or replace damaged bones in her skull.
She was flown to the UK from Pakistan by air ambulance on Monday, almost a week after she and two other schoolgirls were attacked as they returned home from school in Mingora in the Swat Valley.
The gunman who boarded the van in which she was travelling asked for her by name before firing three shots at her.
Malala became widely known as a campaigner for girls' education in Pakistan as a result of a diary she wrote for BBC Urdu about life under the Taliban, when they banned all girls from attending school.
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