The Slovak anti-crime agency NAKA is investigating the envelope, which contained sodium azide when it arrived yesterday, police spokesman Michal Slivka told AFP.
Sodium azide transforms quickly into a potentially deadly gas when mixed with water, an acid or if it comes into contact with metals like copper or lead.
Local media said the envelope had been sent from Sweden.
The Czech ambassador in Bratislava is Livia Klausova, wife of former Czech president Vaclav Klaus, a eurosceptic in power until last year when left-winger Milos Zeman took over.
The three-party, centre-left coalition government has been in power since the early elections of October 2013.