Doha's Ministry of Foreign Affairs added that it condemned all "terrorism acts", in a statement released through the Qatar News Agency last night.
On Monday, Egypt accused fugitive Muslim Brotherhood leaders who fled to Qatar of training and financing those responsible for the deadly bomb attack on the Saint Peter and Saint Paul Church a day earlier.
Cairo's interior ministry pointed a finger at suspect Mohab Mostafa el-Sayed Qassem, also known as "The Doctor", who travelled to Qatar in 2015.
But Qatar said such claims were baseless.
More From This Section
The foreign ministry condemned allegations that Qatar was involved in the bombing on "the pretext that the suspect Mohab Mostafa (el-Sayed Qassem) visited Qatar in 2015".
Ministry spokesman Ahmed Al-Rumaihi said such statements to "sully the name of Qatar" were an attempt to "cover up any failures of the relevant Egyptian authorities" and would inflame tensions.
Qassem visited Qatar on December 3, 2015, "like hundreds of thousands of others who are allowed to enter the country for work or a visit", he said.
Sunday's incident was the deadliest attack in recent memory on Egypt's Christian minority, who make up about 10 percent of the population.
The Islamic State jihadist group claimed responsibility for the attack on Tuesday, and the Muslim Brotherhood has denied any involvement in the bombing.