The exercise, taking place at sea and on the islands around Karlskrona, will gather some 50 military personnel.
"Here in Karlskrona, we will hold drills on finding and disarming homemade bombs, of which we hear in the news almost every day now," Ludvig Adielsson of the Karlskrona Naval Base told Swedish Radio.
Homemade bombs have been found at sea before. One notorious example is the American warship the USS Cole, which tripped on a bomb in Yemen.
"Recently, we have seen terrorist attacks with homemade bombs in Paris, in Turkey and elsewhere, so this is a highly urgent threat to parry," Ludvid Adielsson said.
Residents of Karlskrona have already been briefed on the exercise, which is expected to feature two underwater detonations on the surrounding islands.
In 2010, the first ever suicide attack in Nordic countries was carried out in Sweden, as two bombs went off in central Stockholm. Both Sweden's then-Foreign Minister Carl Bildt and Security Police SÄPO described the bombing as an act of terrorism.
Although Sweden is seldom listed among the terrorists' premier targets, the country's Security Police warned earlier this year of intelligence information about a possible terror threat, whereupon security was raised in airports across the country.
SÄPO has previously identified over 300 people as having left Sweden since 2013 to join the militant jihadists in the Middle East. No less than 135 are believed to have returned to Sweden and currently rank among the biggest threats to the country. Sweden, known for its notoriously lax immigration policy which overlooks radical Islamists, has also been identified as one the EU's foremost "suppliers" of jihadists per capita.