Land border points, airports and ports reinstated passport checks starting Sunday afternoon until US President Barack Obama concludes his visit to Estonia on the evening of September 3.
The restrictions mean that even EU citizens will have to present passports or identification cards at the border. Crossing to Estonia from Latvia is currently only allowed through official border checks.
Kristian Jaani, the head of the police force's North Prefecture, said travelers should expect border crossing to take slightly longer, especially for those arriving by boat.
Ten temporary border check points have been opened on the border with Latvia.
The only previous time Estonia has reinstated pre-Schengen border controls was in 2010, for a meeting of NATO foreign ministers in Tallinn. Estonia has been part of the Schengen Area since 2007, which is composed of 26 European countries that have abolished passport and any other type of border control at their common borders.