"Unfortunately I will not be accompanying the team on this trip," 57-year-old Starkovs said in a statement released by the Latvian Football Federation. "I would like to thank all the fans and journalists who have asked after my health in the last few days. At the moment I am recovering well."
In the absence of Starkovs - an iconic striker in the 1970s and 1980s, when Latvia was part of the USSR - the team will be steered by his assistant Juris Sevlakovs. Starkovs said he would remain in constant contact with the team and was confident his absence would not affect their performance.
"I am convinced the national team will be up to the test in Bratislava," Starkovs said.
Latvia made a bad start last month to their campaign to reach the 2014 finals in Brazil, losing 2-1 to Greece and 4-1 to Group G leaders Bosnia. After the match in Bratislava, they host group minnows Liechtenstein in Riga on Tuesday.