The virus -- rarely fatal, but nevertheless serious -- sparks high fevers and severe joint aches, as well as headaches, nausea and extreme fatigue.
"We are facing a new illness in the country, but we are working to fight it," said El Salvador Health Minister Violeta Menjivar, whose country has reported 1,200 cases so far.
In Panama, two cases have been detected.
It is not yet clear how the virus spread to El Salvador, and its appearance both there and Panama -- two countries with no common border -- has raised fears elsewhere in Central America, especially as the rainy season, most favorable for mosquitoes, is only beginning.
Efforts are already under way to combat the spread of the virus -- including systematic spraying against mosquitoes in El Salvador.
But some countries, including Costa Rica and Nicaragua, are resigned to its eventual emergence, despite increases in border checks aimed at stopping any infected people from crossing.
"We can't stop the chikungunya virus from getting here," Costa Rican health official Roberto Castro said.
"It's not possible to put a mosquito net over the whole country, and many people travel between Costa Rica and the Caribbean."
In Guatemala, the health ministry has raised a preventative alert while suspected cases are analyzed, and Honduras is forming teams to treat the cases it predicts will appear.
In the Caribbean, 16 countries have seen cases since the beginning of June, according to Cuba's state-run newspaper Granma, and the World Health Organization counts 4,500 confirmed cases since the virus first appeared in December 2013.
The chikungunya virus is carried by mosquitoes -- most commonly the Aedes aegypti and Aedes albopictus, which are also responsible for dengue fever.
There is no vaccine or treatment for chikungunya, which has infected millions of people in Africa and Asia since the disease was first recorded in 1952.