The Foreign Ministry said Malta strongly condemned the attack in East Jerusalem yesterday.
According to Reuters, Israeli security forces entered a Jerusalem holy compound and clashed with Palestinian stone throwers on Wednesday.
In expressing solidarity with the victims' relatives, the ministry said Malta reiterated that violence, irrespective of the perpetrator, was unacceptable.
It appealed to all sides to exercise the utmost restraint.
Malta recalled that this attack came only two weeks after a previous one in East Jerusalem.
It urged both parties to return to the negotiating table in as short a time as possible with a view to stem an escalation of violence that risked inflaming the situation further.
The attacks were also condemned by the Nationalist Party.