The Croatian team had been leading 2-1 with just four minutes left of the tie, when a group of their supporters began throwing the flares, with one nearly striking a steward who was attempting to clear the pitch.

While referee Mark Clattenburg halted the match, fans appeared to be fighting in the stands, which could see the country face the risk of disqualification.

It follows the Russian Football Union being given a suspended disqualification, after violence in the crowd following their match with England.

UEFA are expected to launch disciplinary action against the Croatian Football Federation tomorrow, having already been charged by the governing body for setting off of fireworks and pitch invasions by supporters in their opening match against Turkey.

Croatia were last month fined and forced to play their next two 2018 FIFA World Cup qualifiers behind closed doors after two friendly matches were marred by discriminatory chants.

The disruption also appeared to cause Croatia problems on the pitch against the Czech Republic, who were awarded a penalty for a handball by defender Domagoj Vida, in the additional time added on for the disturbances.

Tomas Necid powerfully dispatched the penalty to give the Czech Republic a point they scarcely merited, with the Croatian team having been vastly the superior team.

A powerful left foot shot from Ivan Perisic had given Croatia a 1-0 half-time advantage, before Ivan Rakitic doubled their lead by coolly lofting the ball over Petr Cech after the break, when put through one-on-one with the goalkeeper.

Substitute Milan Skoda surprisingly brought the Czech Republic back into the match after heading in a cross with 15 minutes to play.

The effort and the following crowd trouble halted Croatia’s momentum, with Necid’s late penalty giving the Czech’s their first point of the tournament to give them hope of advancing from the group.

Spain occupy top spot in the group as they pursue a third straight European Championship title, with their second victory of the tournament coming against Turkey.

Alvaro Morata gave the 2008 and 2012 winners the advantage by heading a Nolito cross beyond Turkish goalkeeper Ali Babacan after 34 minutes.

Three minutes passed before Nolito went from provider to scorer as the latched onto a poor header from Mehmet Topal to divert beyond Babacan.

Any hopes of the Turkish fightback were extinguished early in the second half when Morata finished off a flowing Spain move from close range to give his side a 3-0 victory.

Italy became the third team, joining Spain and France, to qualify for the knock-out stage of the tournament after they claimed a narrow 1-0 victory over Sweden in Group E.

A match of few chances saw Italy’s Marco Parolo go closest to breaking the deadlock when he struck the crossbar with seven minutes remaining.

With Sweden looking set to hold out for a second point of the group phase, Eder dashed their hopes when he latched onto a knock down from Zaza to fire Italy to victory and the knock-out stages.