"Events in the southern Mediterranean are dangerous for Europe," Tusk told a press conference after a two-day EU leaders summit in Brussels.
"We condemned the appalling terrorist attack in Tunis this week and agreed to intensify cooperation with Tunisia in order to counter the terrorist threat, to strengthen its promising democracy and to assist its economic and social development," he added.
The attack which left 21 people dead, many of them European tourists, overshadowed the summit where the rapidly deteriorating security situation in neighbouring Libya was a major concern.
Wednesday's assault on the national museum in Tunis was the deadliest since Tunisia's 2011 revolution, which sparked the Arab Spring uprisings and hopes of a more prosperous and democratic future across the region.
Also Read
Many of those hopes have since come to nothing, stoking deep resentment among younger Arabs who see IS and other extremist groups as the only alternative to backward-looking governments.
Mogherini stressed that the EU would work closely with the Tunis government to boost the economy and so offer young Tunisians a future and an alternative to Islamic extremism.
Tusk and Mogherini will also visit Italy and Malta, countries deeply concerned that IS inroads into Libya and North Africa will increase the flood of refugees landing on their shores as they seek to get to Europe.
The EU's 28 leaders at the summit called on Mogherini to begin work on a possible security mission to Libya once the country's warring factions agree a national unity government.