A fresh outbreak of the disease was also detected in Hungary, some 15 kilometres from the Slovak border near Bratislava.
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Inspections against foot-and-mouth disease in Slovakia have caused traffic jams on the D2 highway heading towards the Czech Republic.
Officials reported that tailbacks on both lanes were approximately 12 kilometres long, with Slovak police warning the situation could get worse.
Police said they have advised motorists to use smaller border crossings to travel to the Czech Republic, although drivers should still expect delays there.
In late March, Slovakia declared a state of emergency in a bid to rid the country of foot-and-mouth disease after an outbreak of three cases in separate premises housing cattle.
On Friday, new cases were reported, bringing the total number of affected sites to six.
A fresh outbreak of the disease was also detected in Hungary, some 15 kilometres from the Slovak border near Bratislava.
Border checks and closures
Meanwhile on Monday, the Slovakian government said it had reintroduced temporary border checks with Hungary and Austria in response to the escalating outbreak.
The measure, which came into effect on Tuesday, will remain in place until 8 May, according to Interior Minister Matúš Šutaj Eštok.
"Although the presence of foot-and-mouth disease has not been confirmed in Austria, the measure is necessary due to the proximity of outbreak areas," he said.
Cases of the disease were reported in the Dunajská Streda and Malacky districts, near the Austrian border.
For Hungary, the Slovak interior ministry said it will temporarily close 16 border crossings to ease pressure on police and border staff while veterinarians continue to monitor the situation in the field and the disposal of infected animals.
Foot-and-mouth disease (FMD), a highly contagious viral disease of livestock, mainly affects cattle but can also infect swine, sheep and goats.