JEM says the alleged bombings will cause it to withdraw from the latest round of talks in Doha sponsored by the Qatari government.
"Because of the ongoing comprehensive offensive against the civilian population in Darfur and because of the aggression against our forces on the ground, JEM has decided to freeze its participation in the Doha peace process," said Ahmed Hussein Adam, a spokesman for JEM.
Five other rebel groups announced last weekthat they will take part in the Doha talks.
JEM, which started fighting the Sudanese government in 2003, signed a ceasefire with Khartoum in February and has agreed to a framework for future peace negotiations.
Tensions have escalated in the south since last month's presidential, parliamentary and local elections in Sudan, which many international observers decried as fraudulent.
Salva Kiir, the president of semi-autonomous south Sudan, sent a letter this weekend to Omar al-Bashir, the Sudanese president, expressing concern about military movements.
Kiir said the Sudanese army's manoeuvres in two states - South Darfur and Blue Nile - could inflame tensions in the south.
Separately, a group of mutinous troops from south Sudan's army attacked an army base last week, leaving seven people dead.
The attackers supported a politician, George Athor Deng, who ran for governor of Jonglei state.
The south Sudanese government says the gunmen were angry about Deng's electoral defeat.
A group of eight NGOs, including the Save Darfur Coalition and the Enough Project, published a report last week that warned of renewed war in south Sudan unless the US government pushes the Sudanese government and rebel groups to resume peace talks.