The Australian lawyer, named as Melinda Taylor, was part of a four-member ICC delegation that travelled to the small western mountain town of Zintan to meet Saif al-Islam, who has been held there since his desert capture in November.
The president of the international war crimes court said the four staff members had been detained since Thursday, and demanded their immediate release.
Reflecting Libya's wider problem of powerful local militias and a weak central government, the brigade holding Gaddafi's Western-educated son said it would not heed the government's requests to release the four before questioning them.
Saif al-Islam is wanted by the ICC for crimes from last year's war, but Tripoli wants to try him in his home country.
"During a visit (to Saif al-Islam), the lawyer tried to deliver documents to him, letters that represent a danger to the security of Libya," said Ahmed al-Jehani, the Libyan lawyer in charge of the Saif al-Islam case on behalf of Libya, and who liaises between the government and The Hague-based ICC.
Jehani said the documents were from several people including Saif al-Islam's former right-hand man Mohammed Ismail. He said blank documents signed by Saif al-Islam had also been found.
"She is not in jail. She is being detained in a guesthouse, her colleagues are with her," he told Reuters. Asked whether she would be released soon, Jehani said: "I hope today."
However in Zintan - a small town of 35,000 people - Alajmi Ali Ahmed al-Atiri, the head of the brigade which captured Saif al-Islam, said there were no such plans.
He said "spying and recording" materials had been found when members of the delegation were searched.
The ICC delegation travelled to Libya on Wednesday and had planned to meet Saif al-Islam in Zintan to discuss his defence arrangements, the court said in a statement late on Saturday.
"We are very concerned about the safety of our staff in the absence of any contact with them," ICC President Judge Sang-Hyun Song said in a statement late on Saturday.
"These four international civil servants have immunity when on an official ICC mission. I call on the Libyan authorities to immediately take all necessary measures to ensure their safety and security and to liberate them."
The ICC has previously expressed concern at the conditions under which Saif al-Islam is being held in Libya. Human rights groups have also questioned whether Libya's justice system can meet the standards of international law.
Atiri said the ICC team had asked to meet alone with Saif al-Islam but the request had been declined.
"We tricked the ICC team by presenting them with one of our men who we told them was deaf and old and illiterate but he is actually a wise man who can speak four languages including English," Atiri said.
"That is when we found out the lawyer had a letter written in English that they wanted him to sign admitting that there is no law in Libya and asking to be transferred to the ICC. When we searched the woman we found she had a letter from Mohammed Ismail for Saif and another one written back to Ismail."
Atiri held up two of the documents, one of which he said was a letter from Ismail. He said Ismail's letter had begun with an address that read "Saif al-Islam the joy maker."
"They also took a number of empty papers with his signature on it, and he gave them a number of letters written by Saif for Mohammed Ismail," he said. "Before the delegation entered the meeting with Saif, we inspected them and discovered spying and recording materials on one (member) of the delegation."
Jehani said a pen with a camera and a watch with a recorder were found during the search.
Milad Abdel Nabi, Libya's prosecutor-general in charge of the Saif al-Islam file, said investigations were continuing.
"The case is a homeland security issue ... The lawyer should have presented the material to the prosecutor-general's office before taking it into the suspect," he said.
"Saif would only be allowed private meetings with a lawyer if he had appointed one for himself, but in this case the ICC appointed this lawyer for him and so has no right to sit with Saif privately."
The ICC issued a warrant for Saif al-Islam last year after prosecutors accused him of involvement in the killing of protesters during the revolt that toppled his father.
In May, Libya filed a legal challenge, contesting the court's right to try the case. The ICC ruled this month he could stay in detention in Libya while the court decides if it has the jurisdiction to try him.