The ship, escorted by UK and Danish naval vessels, was dispatched as part of international efforts to remove dangerous stockpiles from the country.
Libyan chemical weapons were destroyed under global supervision in 2014.
But the presence of hazardous materials in the strife-torn country has caused international concern.
Foreign Secretary Boris Johnson said the UK and its international partners were taking “practical and effective action” to eliminate the risks of chemical attacks in Libya.
The items on board the Danish vessel travelling through the Mediterranean are believed to be the last known materials to pose a threat.
Libya has been beset by chaos since NATO-backed forces overthrew long-serving ruler Col Muammar Gaddafi in October 2011, leading to a power vacuum and instability.
Western powers have since become increasingly concerned after so-called Islamic State (IS) built a presence in the North African state. -BBC