Mateu Ginard, head of the regional government's agriculture department, told AFP authorities had decided to declare the entire archipelago a zone affected by Xylella fastidiosa after olive, cherry, almond trees and other plants were found to be contaminated.
"The number of positive results we have is very high," he said, adding exports of live plants had been banned in order to contain any possible spread of the bacteria to the mainland.
Xylella fastidiosa, which emerged in 2013 in southern Italy and has also been detected in France, had until recently not been reported in Spain, the world's top producer of olive oil.
The bacteria was first detected in October last year during a routine check in a garden centre in the island of Majorca, in a cherry tree.
Further checks found more cherry trees affected, and authorities decided to implement a so-called eradication protocol, destroying all plants affected as well as those in a 100-metre radius that could potentially be infected.
Altogether, more than 1,900 were destroyed.
But Ginard said further tests done in Majorca as well as Ibiza, another island in the archipelago, came back positive, indicating the bacteria was more widespread than initially believed.
So far, authorities in the archipelago have detected two strains of the bacteria that are different to the more virulent version that contaminated an estimated one million olive trees in Italy.
But Ginard said the strain that had infected olive trees in the Balearic Islands had yet to be determined.
All were detected in plants in the wild "outside cultivations," he told AFP, and so far farmers have been spared any contamination.
Ginard said that authorities had decided to destroy each and every plant contaminated by the bacteria, which causes some specimens to become stunted, leafless and ultimately lifeless.
But for now, they will forego the eradication protocol as this would imply wiping out all the specimens around the diseased plant, which would be a "disaster" for the archipelago's environment, he added.