Al Sharq Al Awsat said the cartoon "was wrongly interpreted by some" and was aimed at casting a light on the situation which Lebanon finds itself in
Protesters entered the offices of Saudi-owned newspaper Asharq al-Awsat and left papers and upturned chairs on the floor on Friday after the paper published a cartoon depicting the Lebanese flag with the words "an April fool..." written above it.
Inside the flag were the words "the Lebanese state", which form a rhyming pair in Arabic.
Hampered by sectarian tensions, Lebanon has a weak government and has been without a president for almost two years.
The country, which is hosting just over 1 million registered refugees from the conflict in neighbouring Syria, has poor infrastructure and public services.
"Al Sharq Al Awsat regrets the commotion caused by the caricature which was circulated today (Friday) and which was wrongly interpreted by some," the paper said in a statement, saying it respected Lebanon.
"The cartoon aimed to cast light on the situation which the state (Lebanon) finds itself in, as a country which living a big lie caused by attempts to dominate it and distance it from its Arab environment, and to hinder the appointment of a president."