The trail of Islam Salih, whose bureau was closed down by Sudanese authorities in December after filing reports critical of the government, opened in Khartoum on Saturday.
He is accused of defaming the state, circulating false news and preventing a government official from carrying out his duties. The latter charge concerns the customs department.
Lawyer Abd al-Salam al-Jizuli walked out of the trial's first hearing to protest against a court decision to examine two separate lawsuits simultaneously.
"Entering the courtroom, we were surprised that the tribunal would hear both customs and security lawsuits filed separately against Islam Salih, although he was declared to show up today for the hearing into the customs case only," al-Jizuli said.
He said he withdrew after the judge, Umar al-Amin, turned down a request to postpone the hearing so the defence council in the suit filed by the security authority could attend.
"I am defending Salih in the customs case and I cannot represent the defence council in the other case," said the lawyer.
He added that, after his withdrawal, the court also rejected a request for adjournment by Salih who asked for an opportunity to bring his defence council.
"This is a denial of the defendant's right of having defence," said the lawyer.
Al-Jazuli said he would submit a complaint to the head of Khartoum's State Judiciary against the judge, demanding a halt of the trial procedures and the naming of a replacement judge.
Salih said the tribunal, which deals in customs cases only, heard prosecution statements by three customs officers and the legal adviser of the security authority.
"Procedures of the National Security Apparatus against Aljazeera's Khartoum office represent a clear condemnation of the Sudanese political stance towards press freedom"
Aljazeera's Sudan bureau chief
But the men were not cross-examined because of the absence of a defence lawyer.
After hearing the prosecution testimonies, the tribunal announced it would meet again next Thursday to hear the defence witnesses, he said.
But Salih said he was determined to exercise his right to bring in the whole defence council, chaired by lawyer Ali Mahmud Hasanain, who is also a leading official of the opposition Democratic Unionist Party.
He has also denied the charges levelled against him.
"Procedures of the National Security Apparatus against Aljazeera's Khartoum office represent a clear condemnation of the Sudanese political stance towards press freedom," he said.
Launched in 1996, Aljazeera channel has irritated several Arab governments. This has led to the closure of several of its offices in Arab countries in recent years.
After equipment was seized from its Khartoum offices last year, international press freedom bodies were outraged.
Paris-based Reporters Without Borders said: "The seizing of equipment from Aljazeera is just one more indication of the security forces' unacceptable onslaughts on freedom of information, which has been reduced to a sorry state in Sudan.
"Following six suspensions of newspapers in less than four months, now it is the turn of a television channel to be censored on a trumped-up administrative pretext."