It said Jakarta's recent tumultuous election -- which saw hard-line Muslim groups orchestrate the defeat of a Christian governor -- as well the discovery of several terror plots have increased fears of growing intolerance in the country.
As a result, the Christian community sought to counter intolerance by making a greater effort to foster a spirit of religious brotherhood during the holiday, reported ucanews.com.
Archbishop Ignatius Suharyo Hardjoatmodjo of Jakarta, president of the Indonesian bishops' conference, issued a video message to the country's Muslim "brothers and sisters," to mark the end of Ramadan.
"We hope that the sacred moment we celebrate will also be a blessing for all Indonesian people and encourage all citizens in building a more just and prosperous Indonesia," he said.
The Indonesian government set June 25 for Eid al-Fitr this year. Indonesia traditionally celebrates Eid al-Fitr over two days.
Many churches located next to mosques -- including Jakarta's St. Mary of the Assumption Cathedral -- postponed Mass June 25 so as not to interfere with Eid prayers. Catholics -- including bishops, priests, nuns and laypeople -- also visited and greeted Muslims at mosques and in their homes.
Archbishop Antonio Filipazzi, papal nuncio to Indonesia, paid a courtesy call on Indonesian President Joko Widodo after attending Eid prayers at Istiqlal Mosque in Jakarta.
Archbishop Robertus Rubiyatmoko of Semarang visited Muslims attending Eid prayers at Central Java Grand Mosque to foster "fraternity among the people of Indonesia." Other bishops also visited local Muslims leaders.
"I hope that interfaith life in the archipelago, especially in Central Java, will be much better in future, so that peace and joy can be established," Archbishop Rubiyatmoko said.
At churches across Indonesia, Christians offered lunch or gift parcels for poor Muslim families.
In Jakarta, the archdiocese and Community of Sant'Egidio organized an Eid al-Fitr lunch at the Friendship House in West Jakarta for 160 poor Muslim children and their families.
"The poor hardly ever have the chance to sit together for meals. So we invited them so they could sit and eat together," said Piere Doe, coordinator of the event.