Mohamed Atteya, who heads the High Judicial Commission on the Referendum, was responding to calls by an array of secular opposition parties and figures for a "no" vote on Saturday.
"If (the amendments) are rejected, we will face a legislative void, which will be filled by a decree of the Supreme Council of the Armed Forces," Atteya said, referring to the military leadership which took over after Mubarak's resignation last month in the face of a wave of protests.
"The decree of the SCAF may be a constitutional declaration, which would include fundamental principles of public rights and responsibilities, in addition to a text to determine the process by which we will move on to another stage," he said.
"It would not be to amend the constitution. This would be a limited constitutional declaration to govern the transitional period to a new authority, to a modern and civilian state."
A panel appointed by the military council recommended a series of amendments that tackle some of the biggest grievances about the Mubarak-era constitution, but critics say they were drawn up in haste and do not go far enough.
Young militants who spearheaded the 18 days of demonstrations that led to Mubarak's ouster called on Monday for a "no" vote.
Two would-be presidential candidates - Arab League secretary general Amr Mussa and former UN nuclear watchdog chief Mohamed ElBaradei - have also called for the vote to be postponed or scrapped.
Only the powerful Muslim Brotherhood, which was suppressed under Mubarak, and elements of his former ruling National Democratic Party have called for a "yes" vote.
Atteya described the referendum as among "the first fruits of the revolution," and urged the 45 million eligible voters to seize the opportunity to cast their ballot.
"This is the first time in Egyptian history voters would be participating in a political process that is both credible and transparent," he said.
"It is a principal step in the process of democratic transformation to a modern and civil state and the transfer of constitutional powers to a civilian authority elected by the people and the establishment of a new republic that supports the rule of law, equality and justice."
Voters will be required to vote for the amendments as a whole, not individually. They would limit heads of state to two four-year terms, to avoid a repetition of Mubarak's three-decade-long presidency.
They would also ease somewhat the eligibility requirements for presidential candidates.
On polling day, the police will be reinforced by a total of 34,000 troops, 8,000 of them officers.
Atteya said international monitors had been invited to watch the conduct of the voting alongside their Egyptian counterparts.
"The commission is committed to absolute transparency," he said. "We have nothing to hide."