"We have sent initial aid at the request of the heads of the Ukrainian Jewish community to finance purchase of surveillance systems and the protection of Jewish institutions, particularly schools and synagogues," Avi Mayer told AFP.
He said that it was not the agency's role to provide security personnel.
The quasi-governmental agency, which links Jewish communities around the world with Israel and each other, also set up an emergency assistance fund after a March 2011 attack on a Jewish school in the French city of Toulouse, where a gunman shot dead a teacher and three pupils.
"We have a moral responsibility to ensure the safety and security of Ukraine's Jews," a Jewish Agency statement quoted chairman Natan Sharansky as telling colleagues.
"We are in constant contact with the leadership of the Ukrainian Jewish community and are following the events closely," he added.
"The Jewish Agency's assistance aims to increase security at Jewish communal institutions in Ukraine."
Mayer did not say how much money had been sent so far or what the total package would be.
"We have transferred funds and will continue to do so according to need," he said.
Jewish Agency governors will convene during the coming week.
Three months of protest against Ukrainian President Viktor Yanukovych dramatically escalated this week with the deaths of nearly 100 people in clashes between demonstrators and security forces.
The Jewish Agency said that since its creation the emergency assistance fund had disbursed about $4 million (2.9 million euros), "helping to ensure the security of some 50 communities in 25 countries, including... South Africa, Greece, Brazil, Argentina and elsewhere".