A civil society reference group has asked officials of the three non-governmental organisations to ignore the summons by the state regulator.
This comes after the NGOs Co-ordination Board summoned officials of Inuka Kenya whose chief executive officer is former Ethics PS John Githongo, Katiba Institute which is associated with Prof Yash Pal Ghai and Muslims for Human Rights -- groups that have been critical of the Jubilee administration.
The Civil Society Reference Group (CSRG) argues that the regulator headed by Fazul Mahamed as currently constituted, and the Kenya Revenue Authority (KRA) lack the legal and moral authority to regulate organisations registered under the NGO Coordination Act as provided for under Section 4 (1) (i), requiring that such a board must have seven representatives of the NGO Council to constitute a quorum.
"We would, therefore, like to advise public benefit organisations that have been summoned by the Non-Governmental Organisations Co-ordination Board to ignore the summons and this time around seek a court order barring the Board from constantly interfering with their work," said Suba Churchill, the group's presiding convener, in a statement on Sunday.
The crackdown on NGOs deemed to be opposition-friendly is allegedly linked with a move to pre-empt the filing of any petition challenging President Uhuru Kenyatta's re-election before Monday's deadline.
Mr Churchill alleged that the board was usurping the regulatory powers of other government agencies that also regulate not-for-profit organisations in the country and by purporting to summon even organisations that have never been registered under the outdated law, the NGO Board was acting tyrannically in breach of the law.
"This is the only way the affected organisations can avoid being distracted by the NGO Co-ordination Board that has over the years become a nuisance and a puppet at the disposal of the Executive to harass and intimidate the civil society sector," he said.
He alleged that the summons were a cover-up for investigations into the academic qualifications of Mr Mahamed it has since been established that he "did not have the requisite academic qualifications at the time of appointment in to the position".
"These summons are a cover-up for investigations into the academic qualifications of the NGO Board Executive Director Fazul Mohamed by the Ethics and Anti-Corruption Commission (EACC)," said Mr Churchill.
He also faulted the timings of the summons, saying that they were reminiscent of previous attacks on local and international human rights and governance organisations that are perceived to be working to improve the electoral process in Kenya.
He alleged that Katiba Institute was being targeted for litigating on matters of great public interest touching on elections, good governance and accountability by the government and also for challenging in court the constitutionality of the recently passed amendments to the Election Act and the Election Offences Act.
"It is also not lost on the CSRG that Khalef Khalifa and Hassan Abdille, both of Muhuri, were part of the application in the Supreme Court seeking a postponement of the October 26, 2017 repeat presidential election to provide more time for resolution of issues impeding the holding of free, fair, credible and verifiable elections," Mr Churchill said.
At the same time, he claimed that the charges on the three NGOs of failure to comply with tax returns were not different from those that had been levelled against the International Federation of Electoral Systems, the Kenya Human Rights Commission, African Centre for Open Governance (AfriCog), and more recently the International Development Law Organization Kenya office that had been working in partnership with the government since 2009.
"KRA has lost any pretence to autonomy as a tax collector when its senior officials allowed themselves to be used as the registered officials of Friends of Jubilee Foundation, which coincidentally is also registered as an NGO under the NGO Coordination Act," Mr Churchill said.