The protest took place near the Cebu International Convention Centre, one of the venues of the annual Asean and East Asian summit meetings.
Roads near the centre in Cebu were closed to traffic and guarded by riot police as part of a security clampdown.
Police detained the three protesters for questioning after the group refused to heed calls to disperse.
Roads have been closed and tight security
imposed around the summit venue [Reuters]
Abadinas said police were considering filing a complaint of illegal assembly against the three.
Oscar Calderon, the national police chief, has banned rallies near the summit venues for security reasons.
At the summit itself Asean leaders have agreed to write a charter to create a regional bloc similar to the European Union and establish a free trade zone by 2015, according to a draft of their final statement.
The statement, to be issued after the summit concludes on Sunday, also includes an agreement on counterterrorism and the protection of migrant workers.
It seeks to create an "Asean Economic Community" with a free flow of goods, services, investment and capital by 2015. But implementing the goals remains a difficulty.
The 10 countries in Asean have long voiced support for a joint charter, but the process of writing one remains in its initial stages.
One sticking point has been a proposal to allow member states to impose punitive measures on others, reversing a long-standing policy of non-interference in each other's affairs
Measures to tackle terrorism in the region has proved another difficult issue.
According the draft, the leaders have agreed to share information and training on counter-terrorism and cross-border crimes.