The Sacred Heart Church on the Doagh Road was evacuated while a number of suspicious items were examined on Friday.
No controlled explosions were carried out by the army bomb squad but component parts were removed for further forensic examination.
The road, which was closed for a time during the alert, has since reopened and residents allowed to return to their homes.
Parish Priest Father Eugene O'Hagan said the alert disrupted mass at the chapel.
"We had scheduled to have mass at 9.30am on the feast of St Brigid with our own primary school, that of course did not take place," he said.
"There is disruption for us but also it has caused huge disruption for the townsfolk here in Ballyclare."
Sinn Féin MLA for South Antrim Mitchel McLaughlin has called for clarity.
"Questions remain as to whether this was an attack on the church or somebody had abandoned these devices in the grounds.
"The wider community in Ballyclare should have clarity on this and I would urge the PSNI to provide this," he said.
Alliance Newtownabbey Councillor Pat McCudden said: "I am outraged that lives have been put at risk. There can be no justification for leaving a pipe bomb in such a populated area. This is an attack on the church and its congregation."
UUP South Antrim MLA Danny Kinahan also condemned those responsible for the bomb.
"This has been the cause of disruption to local residents and motorists and has required the attention of Army bomb disposal officers," said Mr Kinahan.
"I utterly condemn whoever is responsible for this act. If this does turn out to be an attempt to stoke up sectarian tensions in Ballyclare and elsewhere in south Antrim that is also to be condemned.
"I know that the vast majority of the community in South Antrim has no time for those who would seek to create and exploit sectarian divisions for their own ends."
Police said they are keen to hear from anyone who saw suspicious activity or vehicles in the area over the previous 48 hours.