The Minister for Foreign Affairs has expressed concern to the British government about the intimidation of the Catholic community in Larne, Co Antrim.
Mr Cowen was speaking after meeting the Northern Secretary, Mr Paul Murphy, at Farmleigh, at which the two governments welcomed the peaceful start to the marching season in the North.
While Mr Cowen repeated his call for an statutory inquiry into the murder of the Belfast solicitor Pat Finucane, Mr Murphy did not indicate any change in his government's decision not to proceed with such an inquiry.
Mr Cowen specifically referred to the hospitalisation of the mother of an SDLP councillor in Larne which followed her confrontation with a loyalist gang who were erecting Northern Ireland flags in a mixed area of the town.
Stating that there was a problem with the intimidation of nationalists in Larne, he said the minority community in the town was under particular strain in the wake of the confrontation between loyalists and Ms Rosaleen O'Connor, mother of Councillor Danny O'Connor.
"I would hope that the relevant authorities and local people of influence would use their best endeavours to end these situations of provocation and harassment," said Mr Cowen.
"I ask that people of influence in that area to respect the fact that we're having a reasonably quiet marching season in the sense that it's important that continues and that we have to face down sectarianism."
While no date or location has been fixed for fresh political talks in September, both governments expressed confidence about the process. Mr Cowen said that an end to all forms of paramilitarism was required in the talks as well as decommissioning and a demonstrable commitment to work the power-sharing institutions.
Support for policing from all sides was required, as well as an agreed framework for the devolution of justice and policing powers to the power-sharing Executive.
Mr Cowen said he believed people were "positively engaged" in the run-up to a renewed push for agreement, when asked whether he had any indication that Sinn Féin would use its influence with the IRA to bring about an end to paramilitarism.
The two governments needed to prepare for an intensive engagement with the parties and had a clear sense of what was required from all sides for an overall agreement to be reached.
"Both governments are fully aware of the gap that needs to be breached," Mr Cowen said.
Stating that the parties were seriously and genuinely engaged in the process, Mr Murphy said he believed the talks would succeed. He was still examining the possibility of introducing a form of Truth Commission based on the South African model.
While agreement on such a commission would not necessarily be part of a package of measures in September, he said any success then would greatly aid that discussion.
Also yesterday, Mr Cowen met the president of Sinn Féin, Mr Gerry Adams, in Government Buildings.