"The first information points to a stampede of fans who tried to enter to watch the match between Alianza and FAS" at the Cuscatlán Stadium, the PNC said.
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Salvadoran Health Minister Francisco Alabi said on Twitter that emergency teams had been deployed and the injured were being transferred to local hospitals.
Around 90 people, including minors, are being treated for injuries - most are in "stable" condition, he added.
President Nayib Bukele said an "exhaustive investigation" into the incident would be carried out by the national police and the attorney general's office, CNN reported.
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"Everyone will be investigated: teams, managers, stadium, ticket office, league, federation, etc. Whoever the culprits are, they will not go unpunished," Bukele tweeted.
Video provided by the National Civil Police of El Salvador showed multiple ambulances parked outside the stadium and medics rushing to the scene.
Photos taken from inside the stadium also showed crowds of people, many wearing jersey colors of white and blue.
Alianza and FAS are two of the most popular soccer teams in the Central American country.
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