An official at the Dutch aviation police said on Monday the cargo plane, flying from New York to Frankfurt had lost two cover plates from the fuselage.
The plane landed safely at Amsterdam's Schiphol airport around 1600 GMT on Sunday evening and appeared to have suffered a tyre burst as well.
People living in the neighbourhood of the airport near the Dutch capital had called in with reports of parts falling off the Israeli state-owned airline's plane. Two metal plates have been recovered.
The event brought back painful memories of the 1992 air disaster when an El Al cargo plane crashed shortly after take-off into two high-rise housing blocks in the Bijlmermeer suburb of Amsterdam, killing 43 people.
Rescue workers and surviving residents reported health problems following the event, including fatigue, skin complaints, joint and bone pains, kidney ailments and respiratory problems.
This prompted an inquiry by the Dutch authorities into the plane’s cargo, which was initially claimed by the Israeli airline to be perfumes and gifts.
El Al admitted in 1998 that the plane was also carrying three of the four chemical ingredients needed to make the odourless, highly toxic nerve agent Sarin, the gas Saddam Hussein used against the Kurds in Iraq and which killed a dozen people in the Tokyo metro in 1995.
Men in white suits
The materials, purchased from a US plant, were bound for the Institute for Biological Research in the Israeli town of Ness Ziona south of Tel Aviv.
Israel has never admitted producing chemical or biological weapons and has signed, but not ratified, the International Convention on the Prohibition of Chemical Weapons.
The plane's black box was never found, prompting rumours that members of the Israeli secret service joined the rescue teams undercover to remove any sensitive material.
The appearance of men in white suits sifting through the wreckage added to the air of mystery surrounding the crash.