Mr Puidgemont made the trip just hours after the Belgian immigration minister, Theo Francken, suggested he could be offered asylum over his treatment by Madrid.
The move came as prosecutors back in Spain called for the Catalan leader and his senior ministers, who orchestrated an illegal independence referendum, to be charged with rebellion.
If found guilty he could be sent to jail for 30 years, prompting Mr Francken to infuriate Madrid by claiming that the separatist leader is unlikely to receive a fair trial in Spain.
According to Spanish media Mr Puidgemont is meeting with senior figures in the Flemish nationalist party, which includes Mr Francken, to discuss his next moves.
The Spanish Government sacked him and dissolved the region’s parliament after its MPs voted on Friday to officially declare independence from Madrid and form a new Republic.
Mr Puigdemont is believed to have travelled with other members of the regional Government which was dismissed by the central government in Madrid on Friday.
The Catalan newspaper La Vanguardia is reporting that Mr Puigdemont could make a statement this afternoon whilst in Belgium.
Spain’s Interior Ministry sources have said that they are not “worried” about that trip by Mr Puigdemont to Brussels.
Four of the five Catalan government ministers in Brussels with Carles Puigdemont have been named as Meritxell Borràs, Toni Comin, Joaquim Forn and Dolors Bassa.
The unnamed fifth person is also understood to have been removed following Madrid’s imposition of direct rule following the Catalan Parliament unilateral declaration of independence last Friday.
Ms Bassa was the Minister for Employment and Social Affairs and Mr Forn Catalonia’s Interior Minister.
Mr Comin was in charge of health and Ms Borras was in charge of the areas of governance, public administration and housing.
The trip to Brussels is significant after the the Belgian Secretary of State for Migration and Asylum, Theo Francken, offered political asylum to Mr Puigdemont on Sunday.
The move though caused an uproar within the Belgium government and forced Prime Minister Charles Michel to disavow the head of asylum.
Mr Michel said that the asylum for Mr Puigdemont “is not at all on the agenda” of the Government. I ask Theo Francken not to burn fire.”
The Belgium leader also reiterated his call for dialogue between the Spanish and Catalan authorities.
Earlier today Mr Puigdemont gave the impression that he had defied Madrid’s ruling to dissolve the Catalan Government and posted a picture on his Facebook page from within the government building of the semi-autonomous region.
The post was unclear though and the photo of the inside of the government building in Barcelona was undated and accompanied only by the words “Bon dia” (Good morning) but it would appear that the leader had managed to go to work contravening the rules recently passed by Madrid under Article 155 to dissolve the regional government.
The trip was slammed by the general co-ordinator of the ruling conservative People’s Party Fernando Martínez Maíllo who said it was a “desperate act, nonsense.”
Earlier today the Spanish Attorney General Jose Manuel Maza filed charges of rebellion, sedition and embezzlement against Mr Puigdemont who faces a possible lengthy prison sentence of up to 30 years.
Sources at the regional government told El Nacional that a delegation of MPs, headed by Mr Puigdemont were meeting several Flemish politicians in “a safe and discreet environment”.
There have been suggestions in some media outlets that Mr Puigdemont could apply for political asylum but this has not yet been confirmed.